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PubMed2002

Discrimination and taxonomy of geographically diverse strains of nitrile-metabolizing actinomycetes using chemometric and molecular sequencing techniques.

Mycolic acid-containing actinomycetes capable of metabolizing nitriles were recovered from deep-sea sediments and terrestrial soils by enrichment culture on acetonitrile, benzonitrile, succinonitrile or bromoxynil. A total of 43 nitrile-degrading strains were isolated and, together with previously recovered nitrile-degrading rhodococci, were identified by a polyphasic taxonomic approach, which included mycolic acid profiles, pyrolysis mass spectrometry (PyMS), genomic fingerprinting based on sequence variability of the 16S ribosomal RNA gene using polymerase chain reaction-restriction fragment length polymorphism-single-strand conformational polymorphism, and 16S rRNA gene sequence comparison. Isolates phylogenetically related to Rhodococcus erythropolis dominated the culturable microorganisms from most marine and terrestrial samples. These isolates clustered together in a major pyrogroup that showed high congruence with PRS profiles of the 16S rRNA gene. Such high congruence also was obtained for other recovered isolates that were assigned to species of Rhodococcus and Gordonia. Sequencing data validated the results obtained by PRS analysis and enabled phylogenetic relationships to be established. Some of the recovered bacteria probably represent novel microbial species. The fact that nitrile-metabolizing microorganisms were recovered from a wide range of habitat types suggests that nitrile transforming enzymatic activity is geographically widely distributed in nature.

Actinomycetales↗
PubMed1963

System of color wheels for streptomycete taxonomy.

In the sundry systems of streptomycete taxonomy, color of the sporulating aerial mycelium is frequently employed as a systematic criterion. Color series, each containing species of similar spore colors, are generally erected; however, the range of colors encompassed within a series is often not clearly delineated by the usual word description. Therefore, a system is proposed in which the color content of each series is more accurately defined by means of color tabs. Seven spore-color series are recognized (i.e., red, gray, yellow, blue, green, violet, and white), each of which is represented by a color wheel that displays the range of colors included therein. By comparing spore colors with the color wheels, unclassified isolates can readily be assigned to appropriate color groups.

Color↗
PubMed1992

Review of chemosystematics: multivariate approaches to oral bacteria and yeasts.

There are several problems related to the classification and identification of bacterial and yeast species assigned to the genera Actinobacillus, Haemophilus, Pasteurella, Bacteroides, Prevotella, Porphyromonas, Campylobacter, Wolinella, Treponema, Candida, Torulopsis, and Saccharomyces, most of which belong to the resident oral microflora. The present review was written to demonstrate how multivariate analyses of data on cellular fatty acids, sugars, enzyme activities, and lysis kinetics during ethylenediaminetetraacetic acid (EDTA) and EDTA plus lysozyme treatment can be used to distinguish closely related species of these bacterial and yeast genera. With the exception of the Actinobacillus-Haemophilus-Pasteurella group, fatty acids were more discriminating than sugars. Enzymes from whole cells and outer membrane vesicles also contributed to taxonomic distinction. Apparently, chemosystematics, involving multivariate analyses, is a useful adjunct in oral microbial taxonomy.

Actinobacillus↗
PubMed2000

Human evolution: taxonomy and paleobiology.

This review begins by setting out the context and the scope of human evolution. Several classes of evidence, morphological, molecular, and genetic, support a particularly close relationship between modern humans and the species within the genus Pan, the chimpanzee. Thus human evolution is the study of the lineage, or clade, comprising species more closely related to modern humans than to chimpanzees. Its stem species is the so-called 'common hominin ancestor', and its only extant member is Homo sapiens. This clade contains all the species more closely-related to modern humans than to any other living primate. Until recently, these species were all subsumed into a family, Hominidae, but this group is now more usually recognised as a tribe, the Hominini. The rest of the review sets out the formal nomenclature, history of discovery, and information about the characteristic morphology, and its behavioural implications, of the species presently included in the human clade. The taxa are considered within their assigned genera, beginning with the most primitive and finishing with Homo. Within genera, species are presented in order of geological age. The entries conclude with a list of the more important items of fossil evidence, and a summary of relevant taxonomic issues.

Animals↗
PubMed2006

Guide to blackflies of the Simulium damnosum complex in eastern and southern Africa.

At least 26 members of the Simulium damnosum Theobald complex (Diptera: Simuliidae) are known from eastern Africa, most of which are assumed to be non-anthropophilic and some are restricted to small areas of endemicity. Their discovery was based on polytene chromosome inversion polymorphisms and since then they have been cited as cytological entities, but, in many cases, with inadequate descriptions (e.g. without illustrations of the chromosomes). The present distribution, taxonomy and vector identity have been re-evaluated during the last decade in conjunction with ongoing onchocerciasis control programmes. Here, a summary of the relevant data is presented, integrating results of cytotaxonomic, morphotaxonomic and molecular investigations into a guide that provides a comprehensive system of identification for the cytoforms 'Kagera', 'Kasyabone', 'Kibwezi', 'Kisiwani', 'Kisiwani E', 'Kulfo', 'Linthipe', 'Mombo', 'Mutonga', 'Njombe', 'Nkusi', 'Nkusi SA', 'Nkusi SW', 'Nyika', 'Pienaars', 'Sanje', 'Sebwe', 'Turiani', Simulium damnosum sensu stricto, Simulium kaffaense Hadis et al., Simulium kilibanum Gouteux, Simulium kipengere Krueger, Simulium latipollex (Enderlein), Simulium pandanophilum Krüger, Nurmi & Garms, Simulium plumbeum Krueger, Simulium thyolense Vajime et al. and for five newly recognized molecular forms of 'Nkusi' and S. kilibanum. All taxa except S. pandanophilum are assigned to one of five subcomplexes (damnosum, Ketaketa, Kibwezi, Sanje, squamosum) within the S. damnosum complex. The guide encompasses anthropophilic and non-anthropophilic segregates for the whole of eastern and southern Africa, and is not restricted to larval chromosome criteria; in many cases it also allows the typing of adult flies.

Africa, Eastern↗
PubMed2005

Description, new reconstruction, comparative anatomy, and classification of the Sterkfontein Stw 53 cranium, with discussions about the taxonomy of other southern African early Homo remains.

Specimen Stw 53 was recovered in 1976 from Member 5 of the Sterkfontein Formation. Since its incomplete initial description and comparison, the partial cranium has figured prominently in discussions about the systematics of early Homo. Despite publication of a preliminary reconstruction in 1985, Stw 53 has yet to be compared comprehensively to other Plio-Pleistocene fossils or assessed systematically. In this paper, we report on a new reconstruction of this specimen and provide a detailed description and comparison of its morphology. Our reconstruction differs in important respects from the earlier one, especially in terms of neurocranial length, breadth, and height. However, given that Stw 53 exhibits extensive damage, these dimensions are most likely prone to much error in reconstruction. In areas of well-preserved bone, Stw 53 shares many cranial features with Homo habilis, and we propose retaining it within this species. We also consider the affinities of dental remains from Sterkfontein Member 5, along with those from Swartkrans and Drimolen previously assigned to Homo. We find evidence for sympatry of H. habilis and Australopithecus robustus and possibly Plio-Pleistocene Homo sapiens sensu lato in Sterkfontein Member 5. At Swartkrans and Drimolen, we find evidence of H. habilis. We also compare the morphologies of Stw 53 and SK 847 and find compelling evidence to assign the latter specimen to H. habilis, as has been proposed.

Animals↗
PubMed2005

TaxI: a software tool for DNA barcoding using distance methods.

DNA barcoding is a promising approach to the diagnosis of biological diversity in which DNA sequences serve as the primary key for information retrieval. Most existing software for evolutionary analysis of DNA sequences was designed for phylogenetic analyses and, hence, those algorithms do not offer appropriate solutions for the rapid, but precise analyses needed for DNA barcoding, and are also unable to process the often large comparative datasets. We developed a flexible software tool for DNA taxonomy, named TaxI. This program calculates sequence divergences between a query sequence (taxon to be barcoded) and each sequence of a dataset of reference sequences defined by the user. Because the analysis is based on separate pairwise alignments this software is also able to work with sequences characterized by multiple insertions and deletions that are difficult to align in large sequence sets (i.e. thousands of sequences) by multiple alignment algorithms because of computational restrictions. Here, we demonstrate the utility of this approach with two datasets of fish larvae and juveniles from Lake Constance and juvenile land snails under different models of sequence evolution. Sets of ribosomal 16S rRNA sequences, characterized by multiple indels, performed as good as or better than cox1 sequence sets in assigning sequences to species, demonstrating the suitability of rRNA genes for DNA barcoding.

Animals↗
PubMed2002

[Phylogeny of the Malus (apple tree) species, inferred from its morphological traits and molecular DNA analysis].

Some debated issues of the genus Malus (apple) taxonomy were examined using a variety of species from the collection of the Maikop Experimental Station, Vavilon Research Institute of Plant Industry (Krasnodar krai). Phylogenetic relationships among these species were studied using traditional analysis of morphological traits, RAPD, and complete sequencing of the 5'-internal transcribed spacer (ITS1), 5.8S rRNA, 3'-internal transcribed spacer (ITS2) (constituting a cluster of the rRNA genes), and the terminal fragment of the matK gene encoding chloroplast maturase. The results showed that the Sorbomalus section was polyphyletic; the American apple M. fusca was closely related to the species contributing to the East Asian center of the genus origin, and the American species M. angustifolia, M. coronaria, and M. ioensis were closely related to the M. trilobata relict species, whose assignment to the genus Malus is debated by some authors. Molecular analysis of the species relationships showed that the Middle Asian apple M. sieversii is the species from which apple domestication started.

Asia↗
PubMed1995

Comparative ribosomal protein sequence analyses of a phylogenetically defined genus, Pseudomonas, and its relatives.

I analyzed various families of ribosomal proteins obtained from selected species belonging to the genus Pseudomonas sensu stricto and allied organisms which were previously classified in the genus Pseudomonas. Partial amino acid sequencing of L30 preparations revealed that the strains which I examined could be divided into three clusters. The first cluster, which was assigned to the genus Pseudomonas sensu stricto, included Pseudomonas aeruginosa, Pseudomonas putida, Pseudomonas mendocina, and Pseudomonas fluorescens. The second cluster included Burkholderia pickettii and Burkholderia plantarii. The third cluster, which was a deeply branching cluster in the stem of gram-negative bacteria, included Brevundimonas diminuta and Brevundimonas vesicularis. Despite the different levels of conservation of the N-terminal sequences of ribosomal protein families (the highest level of similarity was 74% for L27 proteins and the lowest level of similarity was 42% for L30 proteins), similar phylogenetic trees were constructed by using data obtained from sequence analyses of various ribosomal protein families, including the S20, S21, L27, L29, L31, L32, and L33 protein families. Thus, I demonstrated the efficacy of ribosomal protein analysis in bacterial taxonomy.

Amino Acid Sequence↗
PubMed1999

[Taxonomy of Citrobacter rods found in human specimens].

The aim of this study was the identification of 181 Citrobacter strains on the basis of the recently proposed taxonomic changes of Brenner. All strains were isolated from diarrhoeic patients; 124 strains were originally sent for identification to Laboratory of Enterobacteriaceae DB NIH, 57 strains was isolated in Czech Republic. Citrobacter isolates were initially identified as C. koseri (3 strains), C. amalonaticus (1 strain) or as members of the C. freundii complex (177 strains). Additionally some biochemical tests were performed. The ability to grow in medium containing KCN, lysine decarboxylase production, lactose fermentation and PYR test were examined. Strains belonging to the C. freundii complex were identified to the species level by biochemical methods on the basis of the results of Brenner, who found some tests to be useful in separating Citrobacter species. These test included citrate and acetate utilization, arginine dihydrolase and ornithine decarboxylase activities, motility, urease production, esculin hydrolysis, and acid production from sucrose, dulcitol, melibiose, raffinose and salicin. On the basis of the criteria described above, 96.6% of the strains tested could be assigned to one of the recently named species of C. freundii complex. Using biochemical tests suggested by Brenner we were able to identify Citrobacter strains members of newly recognised species. A five-test system is proposed to identify the most frequently encountered species currently residing in the C. freundii complex.

Citrobacter↗
PubMedDate not supplied

Progress towards a higher taxonomy of viruses.

The current consensus view is that a higher hierarchical taxonomy of viruses cannot be established for two reasons. Firstly, viruses appear to be polyphyletic in origin, with several sets of viruses arising by different, independent routes at different times. Secondly, subsequent virus adaptation for survival in different host/vector combinations has involved the selective acquisition of additional genes by a process of cassette or modular evolution, with these additional gene modules coming from other viruses or host genetic material. Thus, depending on the gene product used for comparison, different phylogenetic relationships can be deduced. Further virus adaptation can arise by reassortment of segmented genomes, gene duplication, deletions, frameshift mutations, point mutations or de novo development of new gene products from existing, unused reading frames. The solution to the first objection is to place all viruses in a separate kingdom and assign the current viruses to several phyla that reflect these diverse origins. The solution to the second objection is to consider the core module of replication machinery as the major criterion on which to make the initial assignments to classes and orders. For RNA viruses, the major criterion is the sequence identity of the RNA-dependent RNA polymerase. Using this criterion, the positive strand RNA viruses can be assigned to five classes that correspond to the recently recognized supergroups of RNA viruses. These five classes contain four, three, three, three and one order(s) respectively. These fourteen orders contain 31 virus families (including 17 families of plant viruses) and 48 genera (including 30 genera of plant viruses). This approach confirms the separation of the alphaviruses and flaviviruses into two families, the Togaviridae and Flaviridae, but suggests that several other current taxonomic assignments, such as the pestiviruses, hepatitis C virus, rubiviruses, hepatitis E virus and arteriviruses, may be wrong. The coronaviruses and toroviruses appear to be distinct families in distinct orders, not distinct genera of the same family as currently classified. In addition, the luteoviruses are split into two families and apple chlorotic leaf spot virus appears not to be a closterovirus but a new genus of the Potexviridae. From an analysis of the polymerase dendrograms of the dsRNA viruses, it appears that they are not closely related to each other, but belong to four additional classes (Partitiviridae, Reoviridae, Birnaviridae and Cystoviridae) and one additional order (Totiviridae) of one of the classes of positive ssRNA viruses in the same subphylum as the positive strand RNA viruses.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗
PubMed2002

Phylogeny of the family Halomonadaceae based on 23S and 165 rDNA sequence analyses.

In this study, we have evaluated the phylogenetic status of the family Halomonadaceae, which consists of the genera Halomonas, Chromohalobacter and Zymobacter, by comparative 23S and 16S rDNA analyses. The genus Halomonas illustrates very well a situation that occurs often in bacterial taxonomy. The use of phylogenetic tools has permitted the grouping of several genera and species believed to be unrelated according to conventional taxonomic techniques. In addition, the number of species of the genus Halomonas has increased as a consequence of new descriptions, particularly during the last few years, but their features are too heterogeneous to justify their placement in the same genus and, therefore, a re-evaluation seems necessary. We have determined the complete sequences (about 2900 bases) of the 23S rDNA of 18 species of the genera Halomonas and Chromohalobacter and resequenced the complete 16S rDNA sequences of seven species of Halomonas. The results of our analysis show that two phylogenetic groups (respectively containing five and seven species) can be distinguished within the genus Halomonas. Six other species cannot be assigned to either of the above-mentioned groups. Furthermore, Halomonas marina forms a separate branch at a deeper level than the other species of the genus Halomonas, which suggests that it should be ascribed to a separate genus. The genus Chromohalobacter forms a monophyletic group constituted by Chromohalobacter marismortui, the recently reclassified species Chromohalobacter canadensis and Chromohalobacter israelensis and the recently proposed species Chromohalobacter salexigens. Finally, we propose to include the genus Carnimonas, with its single species Carnimonas nigrificans, in the family Halomonadaceae.

Animals↗
PubMed1997

Emended description of Paenibacillus amylolyticus and description of Paenibacillus illinoisensis sp. nov. and Paenibacillus chibensis sp. nov.

The taxonomic position of unidentified group 6 of Bacillus circulans as described by Nakamura and Swezey (L.K. Nakamura and J. Swezey, Int. J. Syst. Bacteriol. 33:46-52, 1983) was determined, and the taxonomy of Paenibacillus amylolyticus was reexamined. The results of PCR amplification of a 16S rRNA gene fragment with a specific primer and comparative analysis of 16S rRNA gene sequences warranted placing the two taxa in the genus Paenibacillus. The levels of DNA reassociation among the strains revealed four groups (designated groups I, II, III, and 6), each with a high level of intragroup relatedness (> 72%). Clustering based on phenotypic characteristics correlated well with DNA relatedness grouping. P. amylolyticus strains were scattered in groups I, II, and III. Strains labeled the type strain of P. amylolyticus from different culture collections appeared in groups I and III. Strains found in group I were identified as P. amylolyticus sensu stricto, and the one strain found in group III was identified as Paenibacillus lautus. Group 6 encompassed strains formerly assigned to B. circulans group 6, and group II contained other strains identified as P. amylolyticus. Groups 6 and II were phenotypically and genetically distinct taxa that were distinguishable from the previously described species. These findings showed that groups 6 and II were new species, for which we propose the names Paenibacillus illinoisensis and Paenibacillus chibensis, respectively.

Bacillus↗
PubMedDate not supplied

Diversity of insect trypanosomatids assessed from the spliced leader RNA and 5S rRNA genes and intergenic regions.

We have determined the sequences of 5S rRNA and spliced leader (SL) RNA genes, and adjacent intergenic regions for representatives of all known trypanosomatid genera parasitizing insects. The genetic loci have been analyzed separately as well as by a combined approach. Several isolates, assigned by morphology to different genera (Leptomonas spp., Blastocrithidia spp.), seem to belong to a single species with an unexpectedly wide host and geographical range. An unnamed trypanosomatid isolated from rats in Egypt was found to belong to the genus Herpetomonas, so far associated with insect hosts only. It is closely related to Herpetomonas ztiplika, a parasite of a blood-sucking biting midge. Apparently several different trypanosomatid species can infect one insect species, as exemplified by Leptomonas sp. PL and Wallaceina sp. Wsd, which were isolated from different specimens of Salda littoralis on the same locality and day. However, since the same species of Leptomonas was obtained from insect hosts belonging to different genera, some insect trypanosomatids may have low host specificity. Our data revealed additional discrepancies between molecular phylogenetic data and cell morphology, rendering current trypanosomatid taxonomy unreliable.

Animals↗
PubMed2000

Strain differentiation in Bacteroides fragilis by RAPD and Dendron computer-assisted gel analysis.

Batteroides fragilis is the anaerobe most frequently isolated from human infections. Strains of this species are not easily distinguished by phenotypic tests. It is important to make this distinction because virulence may vary between strains and because B. fragilis seems to be a heterogeneous species. The aim of this study was to assess the utility of randomly amplified polymorphic DNA (RAPD) analysis for differentiation of 46 strains of B. fragilis. Twenty-seven of the strains belonged to Johnson's DNA homology group I and 8 to group II, while 11 strains had not been assigned to any of these groups (NI group). The primers OPA16 and 18 were chosen among 30 primers tested for optimal RAPD analysis. OPA18 gave best discrimination, revealing a total of 15 genotypes while OPA16 gave 13. The gels obtained after RAPD analysis were evaluated with the Dendron computer-assisted program. Most strains showed similarity levels (S(AB)) within 70%. Strain clusters thus established were not always in agreement with DNA homology since strains from both homology groups fell in the same cluster. Similarly, strains of the NI group fell among the group I and II homology strains. RAPD was useful for differentiation of B. fragilis strains and thus probably suitable for epidemiological studies. On the other hand, DNA-DNA homology, comparing the entire genome of strains rather than a few random priming sites, would be more reliable for taxonomy. Computer-assisted gel analysis made it possible to objectively evaluate multiple banding patterns, thereby increasing the reliability of the RAPD analysis.

Bacteroides Infections↗
PubMed2003

Description of Devosia neptuniae sp. nov. that nodulates and fixes nitrogen in symbiosis with Neptunia natans, an aquatic legume from India.

Neptunia natans is a unique aquatic legume indigenous to tropical and sub-tropical regions and is nodulated symbiotically by rhizobia using an unusual infection process unlike any previously described. Previously, isolates of neptunia-nodulating rhizobia from Senegal were characterized as Allorhizobium undicola. Here we report on a different group of neptunia-nodulating rhizobia isolated from India. Sequencing of the 16S rDNA gene from two of these Indian isolates (strains J1T and J2) show that they belong in the genus Devosia rather than Allorhizobium. Currently, the only described Devosia species is D. riboflavina (family Hyphomicrobiaceae, order Rhizobiales). The complete 16S rDNA sequences of strains J1T and J2 are 95.9% homologous to the type strain, D. riboflavina LMG 2277T, suggesting that these neptunia-nodulating strains from India belong to a new Devosia species. This hypothesis was confirmed by further studies of polyphasic taxonomy (DNA-DNA hybridisation, TP-RAPD patterns, SDS-PAGE of cellular proteins, 16S rDNA RFLP patterns, carbon source utilisation, cellular fatty acid analysis and other phenotypic characterisations), all of which support the proposal that these neptunia-nodulating strains constitute a new Devosia species, which we name Devosia neptuniae sp. nov. These gram negative, strictly aerobic short rods are motile by a subpolar flagellum, positive for catalase, oxidase, urease and beta-galactosidase, can utilise several carbohydrates (but not organic acids) as carbon sources and contain C18:0 3-OH, cis-7 C18:1 11-methyl and cis-7 C18:1 as their major cellular fatty acids. Unlike D. riboflavina, the longer-chain C24:1 3-OH and C26:1 3-OH hydroxy fatty acids are not detected. The type strain of D. neptuniae is LMG 21357T (CECT 5650T). Assignment of this new taxon represents the fourth example in the literature of a non-rhizobial genus of bacteria capable of forming a bonafide dinitrogen-fixing root-nodule symbiosis with legume plants.

Alphaproteobacteria↗
PubMed2005

Comparative performance of the 16S rRNA gene in DNA barcoding of amphibians.

BACKGROUND: Identifying species of organisms by short sequences of DNA has been in the center of ongoing discussions under the terms DNA barcoding or DNA taxonomy. A C-terminal fragment of the mitochondrial gene for cytochrome oxidase subunit I (COI) has been proposed as universal marker for this purpose among animals. RESULTS: Herein we present experimental evidence that the mitochondrial 16S rRNA gene fulfills the requirements for a universal DNA barcoding marker in amphibians. In terms of universality of priming sites and identification of major vertebrate clades the studied 16S fragment is superior to COI. Amplification success was 100% for 16S in a subset of fresh and well-preserved samples of Madagascan frogs, while various combination of COI primers had lower success rates.COI priming sites showed high variability among amphibians both at the level of groups and closely related species, whereas 16S priming sites were highly conserved among vertebrates. Interspecific pairwise 16S divergences in a test group of Madagascan frogs were at a level suitable for assignment of larval stages to species (1-17%), with low degrees of pairwise haplotype divergence within populations (0-1%). CONCLUSION: We strongly advocate the use of 16S rRNA as standard DNA barcoding marker for vertebrates to complement COI, especially if samples a priori could belong to various phylogenetically distant taxa and false negatives would constitute a major problem.

Journal Article↗
PubMed2006

Pathology and preliminary characterization of a parapoxvirus isolated from a California sea lion (Zalophus californianus).

Cutaneous pox-like lesions are a common complication in the rehabilitation of pinnipeds. However, the exact identity, taxonomy, and host range of pinniped parapoxviruses remain unknown. During a poxvirus outbreak in May 2003 in California sea lions (Zalophus californianus) at a marine mammal rehabilitation facility, multiple raised, firm, 1-3-cm skin nodules from the head, neck, and thorax of one sea lion weanling pup that spontaneously died were collected. Histologically, the nodules were characterized by inflammation and necrosis of the dermis and epidermis, acanthosis, and ballooning degeneration of the stratum spinosum. Large, coalescing eosinophilic cytoplasmic inclusions were observed in the ballooned cells. A parapoxvirus (sea lion poxvirus 1, SLPV-1) was isolated on early passage California sea lion kidney cells inoculated with a tissue homogenate of a skin nodule. The morphology of the virions on electron microscopy was consistent with that of parapoxviruses. Partial sequencing of the genomic region encoding the putative major virion envelope antigen p42K confirmed the assignment of the sea lion poxvirus to the genus Parapoxvirus. Although SLPV-1 is most closely related to the poxvirus of harbor seals of the European North Sea, it is significantly different from orf virus, bovine papular stomatitis virus, pseudocowpox virus and the parapoxvirus of New Zealand red deer.

Amino Acid Sequence↗