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PubMed2000

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

It is important to distinguish between Bacteroides fragilis strains as their virulence may vary and as B. fragilis seems to be a heterogeneous species. The aim of our study was to evaluate ribotyping for differentiation of 46 strains of B. fragilis and for assessment of strain heterogeneity within and between the two DNA-DNA homology strain groups established in this species. Twenty-seven strains belonged to Johnson's DNA homology group I and eight to group II. Eleven strains had not been assigned to any group (NI group). DNA from all strains was cut with BglI, EcoRI and HindIII. Restriction fragment length polymorphisms were investigated using a non-radioactive digoxigenin-labelled cDNA probe transcribed from Escherichia coli 16S+23S rRNA. Ribotyping with BglI was most discriminatory, revealing a total of 26 different patterns by visual inspection of gels. EcoRI followed with 20 patterns and HindIII with 13 patterns. The gels from ribotyping were processed using the Dendron computer-assisted program. Strain clusters established using Dendron were not always in agreement with homology-based strain groups. Strains of the NI group fell into both homology groups. Ribotyping, as it is based on a relatively small portion of the genome, is useful for strain distinction in epidemiological studies with B. fragilis, whereas DNA-DNA homology, using the entire genome, is more reliable for taxonomy. The Dendron computer-assisted program, which enabled objective assessment of multiple banding patterns, increased the reliability of ribotyping.

Bacteroides fragilis↗
PubMed2005

Paragonimus skrjabini Chen, 1959 (Digenea: Paragonimidae) and related species in eastern Asia: a combined molecular and morphological approach to identification and taxonomy.

A molecular and morphometric investigation is reported on the species complex of mammalian lungflukes of which Paragonimus skrjabini Chen, 1959 and P. miyazakii Kamo, Nishida, Hatsushika & Tomimura, 1961 are the best-known examples. This species complex (here called the P. skrjabini complex) is shown to be monophyletic using DNA sequences from the nuclear ITS2 region and the mitochondrial cox1 gene. The latter marker permits the discrimination of populations, some previously named as distinct species, from various geographical locations in China and Japan. Morphometric analysis of a number of variables accords remarkably closely with the molecular results. Main findings are that (1) nominal P.skrjabini from Fujian Province in eastern China is phylogenetically very close to P. miyazakii from Japan. It is proposed that both taxa should be referred to the same subspecies as P. krjabini miyazakii. (2) Populations from Guangdong Province, Guangxi Zhuang Autonomous Region, Sichuan and Hubei should be referred to P. skrjabini skrjabini. Specimens of P. skrjabini from the Yangtze basin in Sichuan and Hubei are remarkably similar to one another according to genetic and morphometric data, but are not so different from Guangdong populations that they should be referred to a different subspecies at this stage. Specimens of P. skrjabini from Yunnan have not been assigned to a subspecies at this stage. (3) Partly following earlier studies, we regard the following as synonyms of P. skrjabini: P. miyazakii (reduced to subspecific status); P. szechuanensis Chung & Tsao, 1962 (probably belongs to P. s. skrjabini); and P. hueitungensis Chung, Hsu, Ho, Kao, Shao, Chiu, Pi, Liu, Ouyang, Shen, Yi & Yao, 1975 (probably belongs to P.s.skrjabini ); P. veocularis (Chen & Li, 1979) (specimens from Fujian regarded as belonging to this species should be referred to P.skrjabini miyazakii: the subspecific status of specimens from the type-locality in northern Sichuan is unclear). A number of questions remain unresolved. The name P. hokuoensis Ho & Chung, 1964 was proposed for two individual metacercariae of distinctive appearance from southern Yunnan. DNA sequences from very similar metacercariae from the same locality place this nominal species within, or sister to, the P. skrjabini complex. As yet, nothing is known regarding adult morphology or biology of this taxon and we retain it here as a distinct species. P. heterorchis (Zhou, Pang & Hsiang, 1982) might be a synonym of P. skrjabini: the form of the metacercaria provides evidence against this view and further work is required. P. macrorchis Chen, 1962 has probably been confused with P. skrjabiniin China. Within China, the former probably occurs only on Hainan Island, although P. fukienensis Tang & Tang, 1962 from Fujian Province could be a synonym.

Animals↗
PubMed1999

Prototheca richardsi, a pathogen of anuran larvae, is related to a clade of protistan parasites near the animal-fungal divergence.

Prototheca richardsi is a protist of uncertain taxonomy which mediates growth inhibition in anuran larvae. Cells of P. richardsi were isolated from tadpole faeces and DNA was purified by Qiagen chromatography. Nuclear small-subunit (18S) rDNA (ssu-rDNA) was amplified by PCR using universal primers, cloned, and six clones (two from each of three separate isolates) were sequenced. All clones yielded an essentially identical sequence of 1802 nucleotides. In situ hybridization of fluorescent Prototheca-specific oligonucleotide probes, designed using the derived 18S rDNA sequence, confirmed that the sequence was indeed from P. richardsi cells and not from other components of tadpole faeces. The P. richardsi sequence was aligned with ssu-rDNA from a range of other eukaryotes, and phylogenetic analyses were carried out using several inference methods. P. richardsi consistently and stably grouped within a novel clade that contains rDNAs from an apparently heterodisperse group of parasitic micro-organisms assigned to the class Ichthyosporea. P. richardsi is evidently misplaced in the genus Prototheca, and the authors propose its inclusion in a new genus Anurofeca.

Animals↗
PubMed1989

The utility of cognitive coping strategies for altering pain perception: a meta-analysis.

The literature on the utility of cognitive coping strategies in pain control has been unclear because of 2 principal limitations: the lack of a validated classification system, and reliance on qualitative and quasi-statistical reviews. In this study, an empirically based multidimensional taxonomy was employed to categorize the variety of cognitive coping strategies into 6 major classes: external focus of attention, neutral imaginings, pleasant imaginings, dramatized coping, rhythmic cognitive activity and pain acknowledging. Meta-analytic techniques were introduced to evaluate the overall efficacy of cognitive strategies (in comparison to no-treatment controls), the relative efficacy of these strategies (how the different groups of strategies compare with one another), and the substantive efficacy of such strategies (how cognitive strategies fare against placebo/expectancy conditions). Results revealed that, in general, cognitive coping strategies are more effective in alleviating pain as compared to either no-treatment or expectancy controls. Each individual class of strategies significantly attenuates pain although the imagery methods are the most effective whereas pain acknowledging is the least effective. Positive expectancy is no better than no treatment. These findings stand in contrast with previous reviews that have not assigned prime importance to imagery or for that matter have not shown cognitive strategies to be particularly effective. Results are discussed with reference to attentional models and methodological issues.

Adaptation, Psychological↗
PubMed1978

Physiological and biochemical contributions to the taxonomy of the genus Chlorella. XI. DNA hybridization.

1. DNA homology was studied in 12 Chlorella species. The DNA of 88 strains was hybridized with 3H-labelled DNA from C. fusca var. vacuolata 211-8 b and from C. vulgaris 211-8m. The results indicate that the genus Chlorella is a heterogenous taxon which consists of several groups of species. 2. The "C. fusca group" comprises C. fusca var. vacuolata, C. fusca var. rubescens, and C. zofingiensis. Within this group, C. zofingiensis appears to be more closely related to C. fusca var. vacuolata than is C. fusca var. rubescens. C. fusca var. fusca does not belong to this group of taxa. 3. The "C. vulgaris group" consists of C. vulgaris, C. sorokiniana, and C. saccharophila. There are several strains which seem to assume a position intermediate between C. vulgaris and C. saccharophila. C. protothecoides is not related to this group of species. 4. Several groups of strains of C. sorokiniana with different base compositions (guanine + cytosine content) of their DNA appear to belong to the same taxon. 5. In addition to C. fusca var. fusca and C. protothecoides, also C. luteoviridis, C. minutissima, C. kessleri, and C. homosphaera seem to have so little relationship with the other species that their assignment to the genus Chlorella appears questionable.

Chlorella↗
PubMed2006

Molecular phylogeny of Clupeiformes (Actinopterygii) inferred from nuclear and mitochondrial DNA sequences.

The taxonomy of clupeiforms has been extensively studied, yet phylogenetic relationships among component taxa remain controversial or unresolved. Here we test current and new hypotheses of relationships among clupeiforms using mitochondrial rRNA genes (12S and 16S) and nuclear RAG1 and RAG2 sequences (total of 4749bp) for 37 clupeiform taxa representing all five extant families and all subfamilies of Clupeiformes, except Pristigasterinae, plus seven outgroups. Our results, based on maximum parsimony, maximum likelihood, and Bayesian analyses of these data, show that some traditional hypotheses are supported. These include the monophyly of the families Engraulidae, consisting of two monophyletic subfamilies, Engraulinae (Engraulis and Anchoa) and Coilinae (Coilia and Setipinna), and Pristigasteridae (here represented only by Ilisha and Pellona). The basal position of Denticeps among clupeiforms is consistent with the molecular data when base compositional biases are accounted for. However, the monophyly of Clupeidae was not supported. Some clupeids were more closely related to taxa assigned to Pristigasteridae and Chirocentridae (Chirocentrus). These results suggest that a major revision in the classification of clupeiform fishes may be necessary, but should await a more complete taxonomic sampling and additional data.

Animals↗
PubMed1972

Taxonomy of aerobic marine eubacteria.

Two hundred and eighteen strains of nonfermentative marine bacteria were submitted to an extensive morphological, physiological, and nutritional characterization. All the strains were gram-negative, straight or curved rods which were motile by means of polar or peritrichous flagella. A wide variety of organic substrates served as sole sources of carbon and energy. The strains differed extensively in their nutritional versatility, being able to utilize from 11 to 85 carbon compounds. Some strains had an extracellular amylase, gelatinase, lipase, or chitinase and were able to utilize n-hexadecane and to denitrify. None of the strains had a yellow, cell-associated pigment or a constitutive arginine dihydrolase system, nor were they able to hydrolyze cellulose or agar. The results of the physiological and nutritional characterization were submitted to a numerical analysis which clustered the strains into 22 groups on the basis of phenotypic similarities. The majority of these groups were separable by a large number of unrelated phenotypic traits. Analysis of the moles per cent guanine plus cytosine (GC) content in the deoxyribonucleic acid of representative strains indicated that the peritrichously flagellated groups had a GC content of 53.7 to 67.8 moles%; polarly flagellated strains had a GC content of 30.5 to 64.7 moles%. The peritrichously flagellated groups were assigned to the genus Alcaligenes. The polarly flagellated groups, which had a GC content of 43.2 to 48.0 moles%, were placed into a newly created genus, Alteromonas; groups which had a GC content of 57.8 to 64.7 moles% were placed into the genus Pseudomonas; and the remaining groups were left unassigned. Twelve groups were given the following designations: Alteromonas communis, A. vaga, A. macleodii, A. marinopraesens, Pseudomonas doudoroffi, P. marina, P. nautica, Alcaligenes pacificus, A. cupidus, A. venustus, and A. aestus. The problems of assigning species of aerobic marine bacteria to genera are discussed.

Alcaligenes↗
PubMed2006

Was Australopithecus anamensis ancestral to A. afarensis? A case of anagenesis in the hominin fossil record.

We tested the hypothesis that early Pliocene Australopithecus anamensis was ancestral to A. afarensis by conducting a phylogenetic analysis of four temporally successive fossil samples assigned to these species (from earliest to latest: Kanapoi, Allia Bay, Laetoli, Hadar) using polarized character-state data from 20 morphological characters of the dentition and jaws. If the hypothesis that A. anamensis is ancestral to A. afarensis is true, then character-state changes between the temporally ordered site-samples should be congruent with hypothesized polarity transformations based on outgroup (African great ape) conditions. The most parsimonious reconstruction of character-state evolution suggests that each of the hominin OTUs shares apomorphies only with geologically younger OTUs, as predicted by the hypothesis of ancestry (tree length=31; Consistency Index=0.903). This concordance of stratigraphic and character-state data supports the idea that the A. anamensis and A. afarensis samples represent parts of an anagenetically evolving lineage, or evolutionary species. Each site-sample appears to capture a different point along this evolutionary trajectory. We discuss the implications of this conclusion for the taxonomy and adaptive evolution of these early-middle Pliocene hominins.

Animals↗
PubMedDate not supplied

Quantitative histologic factors for grouping childhood supratentorial neuroglial tumors.

The histologic heterogeneity of childhood supratentorial neuroglial tumors, when quantified, identifies relatively homogeneous subgroups for prognostic purposes and for assignment in clinical trials. Our sample consisted of supratentorial tumors in the Childhood Brain Tumor Consortium. The data consist of reliably identified histologic features and demographic, clinical, operative, and survival information. Factor analysis was used to identify uncorrelated "factors," each represented by a different combination of histologic features in 703 tumors. The defining histologic features were used to label each factor. The heterogeneity of each tumor was summarized using the factor scores for each factor. We compared the survival estimates of subgroups of tumors within common diagnostic classes. We identified five uncorrelated quantitative factors that accounted for much of the histologic variation. Our factor labels were Jumbo, Fibrillary, Proliferative, Spongy, an Oligodendroglial. Two thirds of tumors had high scores on two or more factors, indicating a high degree of heterogeneity among these tumors. Eighty-four percent of supratentorial tumors were accounted for by 19 nonoverlapping relatively homogeneous histologic groups. The five quantitative factors complement standard qualitative taxonomies by summarizing more completely the histologic feature aspects of a tumor than by diagnosis alone and quantify the histologic heterogeneity of individual tumors. Histologically homogeneous groups of tumors are essential for clinical trials, biologic research, and prognostic models.

Adolescent↗
PubMed1992

Proposed minimal standards for the genus Mycobacterium and for description of new slowly growing Mycobacterium species.

In accordance with Recommendation 30b of the International Code of Nomenclature of Bacteria, which calls for the development of recommended minimal standards for describing new species, we propose minimal standards for describing the genus Mycobacterium and new slowly growing species of this genus. The minimal standards for assignment of a strain to the genus Mycobacterium include acid-alcohol fastness, a DNA G+C content in the range from 61 to 71 mol%, and mycolic acid detection with characterization of C22 to C26 pyrolysis esters. The recommended minimal standards for describing a new slowly growing Mycobacterium species are based on the results of phenotypic and genomic studies and include the results of the following conventional tests: growth at 25, 30, 33, 37, 42, and 45 degrees C; pigmentation; resistance to isoniazid, thiophene-2-carboxylic acid hydrazide, hydroxylamine, p-nitrobenzoic acid, sodium chloride, thiacetazone, picrate, and oleate; catalase activity; Tween hydrolysis; urease activity; niacin detection; and nitrate reductase, acid phosphatase, arylsulfatase, pyrazinamidase, and alpha-esterase activities. In addition, a mycolic acid profile should be determined, and DNA-DNA hybridization experiments in which the difference between the denaturation temperature of the homologous reaction and the denaturation temperature of the heterologous reaction is determined should be performed. This proposal has been endorsed by the members of the Subcommittee for Taxonomy of the Mycobacteria of the International Committee on Systematic Bacteriology.

Base Composition↗
PubMed1991

Identification of a plant-derived mollicute as a strain of an avian pathogen, Mycoplasma iowae, and its implications for mollicute taxonomy.

Strain PPAV, a filamentous but nonhelical mollicute, was isolated from aborted apple seeds in France in late 1979. This organism grew well in SP-4 broth, fermented glucose, and required sterol for growth, and most of its properties suggested that it belonged to the genus Mycoplasma. However, it was serologically distinct; in addition, unlike other Mycoplasma species, genome measurements consistently yielded values of about 1,000 MDa (ca. 1,500 kbp), and the organism had a growth temperature optimum of 43 degrees C. A comparison of strain PPAV 16S rRNA sequences with those of other mollicutes revealed a high degree of sequence similarity to a strain of Mycoplasma iowae, which is commonly encountered in poultry. This relationship was confirmed by performing a restriction endonuclease pattern analysis and DNA-DNA hybridization tests. The genome size of type strain 695 of M. iowae was determined to be about 1,000 MDa (1,500 kbp) by renaturation kinetics, a value which is much higher than any other value known in the genus. Additional measurements by pulsed-field gel electrophoresis yielded values of 1,300 kbp for both strain PPAV and M. iowae. Subsequent phenotypic comparisons supported this relationship. Serologic tests with strain PPAV and other strains of M. iowae confirmed the findings of other investigators that this species is serologically heterogeneous. The high optimum temperature for growth of strain PPAV was also shared by a number of M. iowae isolates. Genome size is an inappropriate character for taxonomic assignment to the family Mycoplasmataceae because strain PPAV and other established species in this family are now known to have genomes ranging in size from 1,000 to 1,400 kbp.

Animals↗
PubMed1994

Diagnosis of narcissistic self-esteem regulation in patients with factitious illness (Munchausen syndrome).

A quantitative taxonomy for the identification of patients with narcissistic pathology and with borderline personality disorders based on test results is presented. The quantitative identification of these subgroups was produced using a Q-factor analysis. Based on the correlation of the subjects by means of the 241 questions from the narcissistic inventory of Deneke and Müller [27], three subgroups could be defined. Two of these groups exhibited a pathology of the self-system which corresponded to the pathology described by Kernberg [24] for narcissistic and borderline personality disorders. The third group is characterized by reduced observable self-pathology traits from the narcissistic inventory. By means of the reclassification of these three taxonomical groups with the discriminant analysis, two discriminant functions could be calculated, using the weighting of the single test scales for a classification of new patients. These classification functions were used to examine 18 patients suffering from factitious disorders. The evaluation of test profiles with the reduced narcissistic inventory of Deneke and Müller [11] in order to identify the three taxonomical groups showed that 9 patients (50%) had a borderline personality disorder and 6 patients (33%) a narcissistic personality disorder, while 3 patients (17%) could be assigned to the subgroup without self-pathology. In summary, 83% of the examined patients with factitious disorders exhibited a disorder in self-regulation. The previous clinical observations of self-regulation for patients with factitious disorders could thus be confirmed. It becomes clear that different high levels of disorder in self-regulation (position in the sphere of the discriminant function) correspond to varying degrees of prognostic significance.

Adult↗
PubMed1993

Longitudinal study of relations between human salivary antimicrobial proteins and measures of dental plaque accumulation and composition.

Many studies have attempted to relate levels of antimicrobial proteins in saliva to oral health; results have been inconsistent, and one reason might be inconsistency of measures of plaque and saliva within subjects. This study investigated associations between plaque and salivary variables in longitudinal data. Whole saliva, and 8-h plaque pooled from buccal first permanent molars, was obtained from 32 dental students on Tuesdays from 3:00-6:00 p.m. over 4 weeks. Salivary flow rate was determined, and samples were assayed for lysozyme, lactoferrin, total peroxidase, myeloperoxidase, OSCN-, sIgA and total protein. Colonies on mitis-salivarius agar were assigned to Streptococcus sanguis, Strep. mutans or Strep. salivarius on the basis of morphology, supplemented by the API Rapid Strep identification system. Consistency of values within subjects across weeks was evaluated by repeat-measures analysis of variance and intraclass correlation; data were transformed to reduce skewness. Pearson's r was used to determine associations between plaque and salivary variables. Significant intraclass correlations (alpha = 0.05) were found for all salivary variables except myeloperoxidase, and for total flora, total streptococci, Strep. sanguis and Strep. sanguis as a proportion of total streptococci. Significant Pearson correlations with Strep. sanguis as a proportion of total streptococci were found for total protein (r = -0.24), sIgA (r = -0.22), lactoferrin (r = -0.19) and OSCN- (r = 0.20) when data from all weeks were pooled (n = 128). Strep. sanguis proportions tended to be low in subjects with high values for salivary proteins; the range of proportions was wider in subjects with low salivary values. These findings suggest some consistency of weekly values for many plaque and salivary variables. They also support previous cross-sectional data which suggested that salivary antimicrobial proteins may have some effect on plaque composition. This study was made before recent revisions in streptococcal taxonomy, and further research is needed to clarify interactions of salivary proteins with currently defined species.

Bacteria↗
PubMed2005

Transfer of Pectobacterium chrysanthemi (Burkholder et al. 1953) Brenner et al. 1973 and Brenneria paradisiaca to the genus Dickeya gen. nov. as Dickeya chrysanthemi comb. nov. and Dickeya paradisiaca comb. nov. and delineation of four novel species, Dickeya dadantii sp. nov., Dickeya dianthicola sp. nov., Dickeya dieffenbachiae sp. nov. and Dickeya zeae sp. nov.

A collection of 75 strains of Pectobacterium chrysanthemi (including all biovars and pathovars) and the type strains of Brenneria paradisiaca (CFBP 4178(T)) and Pectobacterium cypripedii (CFBP 3613(T)) were studied by DNA-DNA hybridization, numerical taxonomy of 121 phenotypic characteristics, serology and 16S rRNA gene-based phylogenetic analyses. From analysis of 16S rRNA gene sequences, it was deduced that P. chrysanthemi strains and B. paradisiaca CFBP 4178(T) formed a clade distinct from the genera Pectobacterium and Brenneria; therefore, it is proposed to transfer all the strains to a novel genus, Dickeya gen. nov. By DNA-DNA hybridization, the strains of P. chrysanthemi were distributed among six genomic species: genomospecies 1 harbouring 16 strains of biovar 3 and four strains of biovar 8, genomospecies 2 harbouring 16 strains of biovar 3, genomospecies 3 harbouring two strains of biovar 6 and five strains of biovar 5, genomospecies 4 harbouring five strains of biovar 2, genomospecies 5 harbouring six strains of biovar 1, four strains of biovar 7 and five strains of biovar 9 and genomospecies 6 harbouring five strains of biovar 4 and B. paradisiaca CFBP 4178(T). Two strains of biovar 3 remained unclustered. Biochemical criteria, deduced from a numerical taxonomic study of phenotypic characteristics, and serological reactions allowed discrimination of the strains belonging to the six genomic species. Thus, it is proposed that the strains clustered in these six genomic species be assigned to the species Dickeya zeae sp. nov. (type strain CFBP 2052(T)=NCPPB 2538(T)), Dickeya dadantii sp. nov. (type strain CFBP 1269(T)=NCPPB 898(T)), Dickeya chrysanthemi comb. nov. (subdivided into two biovars, bv. chrysanthemi and bv. parthenii), Dickeya dieffenbachiae sp. nov. (type strain CFBP 2051(T)=NCPPB 2976(T)), Dickeya dianthicola sp. nov. (type strain CFBP 1200(T)=NCPPB 453(T)) and Dickeya paradisiaca comb. nov., respectively.

Animals↗
PubMed2005

Geobacillus jurassicus sp. nov., a new thermophilic bacterium isolated from a high-temperature petroleum reservoir, and the validation of the Geobacillus species.

Four thermophilic, spore-forming bacterial strains, DS1(T), DS2, 46 and 49, were isolated from the high-temperature Dagang oilfield, located in China. The strains were identified by using the polyphasic taxonomy approach. These were aerobic, gram-positive, rod-shaped, moderately thermophilic (with an optimum growth temperature of 60-65 degrees C), chemoorganotrophic bacteria capable of growing on various sugars, carboxylic acids and crude oil. Two strains, DS1(T) and DS2, were capable of growing on individual saturated hydrocarbons. The G + C content of the DNA of strains DS1(T) and DS2 was 54.5 and 53.8 mol%, respectively. The phylogenetic analysis of the 16S rDNA of strains DS1(T) and DS2 showed that they form a separate cluster within the genus Geobacillus. The cellular fatty acids of the isolates were dominated by iso-15:0, iso-16:0 and iso-17:0 acids, which are the typical fatty acids of bacteria from the genus Geobacillus. The DNA-DNA hybridization study and the comparative analysis of the morphological and chemotaxonomic characteristics of strains DS1(T) and DS2 showed that they differ from the previously described Geobacillus species and belong to a new species, which was called Geobacillus jurassicus. DS1(T) (=VKM B2301(T), = DSM 15726(T)) is the type strain of this species. According to both DNA-DNA reassociation studies and 16S rDNA sequence analysis, two other strains, 46 and 49, were assigned to the species G. stearothermophilus. In this paper, we provide evidence that the new combinations G. stearothermophilus, G. thermoleovorans, G. kaustophilus, G. thermoglucosidasius and G. thermodenitrificans may be considered to be valid.

Aerobiosis↗
PubMed1993

Serovar determination and molecular taxonomic correlation in Mycobacterium avium, Mycobacterium intracellulare, and Mycobacterium scrofulaceum: a cooperative study of the International Working Group on Mycobacterial Taxonomy.

A cooperative study was conducted by the International Working Group on Mycobacterial Taxonomy to correlate the agglutination serovar designations of Mycobacterium avium, Mycobacterium intracellulare, and Mycobacterium scrofulaceum strains with the species ascriptions of these organisms according to molecular criteria and cultural properties and to assess the reproducibility of serovar determinations for a set of 63 reference strains of these species. Among the molecular criteria, the level of agreement between results obtained with nucleic acid probes and T-catalase serology results was 94% for strains of M. avium and M. intracellulare. Nucleic acid probes were not available for M. scrofulaceum, but none of the 10 strains ascribed to this species on the basis of catalase serology data reacted with a nucleic acid probe for M. avium or M. intracellulare. Ascription to a species on the basis of mycolic acid high-performance liquid chromatography patterns was in agreement with catalase serology results in 86% of the cases examined. Most strains belonging to serovars 1 through 6 and 8 through 11 were identified by molecular criteria as M. avium, most strains belonging to serovars 7, 12 through 20, 23, and 25 were identified as M. intracellulare, and most strains belonging to serovars 41 through 43 were identified as M. scrofulaceum, in agreement with common current practice. Evidence for assigning serovar 27 to M. scrofulaceum was obtained. However, two strains of a given serovar may, on occasion, be placed in different species. The dominant species assignments for strains belonging to serovars 21, 24, 26, and 28 remain unresolved.(ABSTRACT TRUNCATED AT 250 WORDS)

Agglutination Tests↗
PubMed1997

Molecular taxonomy and epidemiology of Blastomyces and Histoplasma species.

Cladistic analysis of partial 26S rRNA sequences was used to estimate evolutionary distances among species and varieties of the dimorphic onygenalean genera Blastomyces, Coccidioides, Emmonsia, Histoplasma and Paracoccidioides. With the exception of Coccidioides, all genera were closely related, with about 5% base differences and even less (1-2%) between Blastomyces and Emmonsia. These data were supported by a teleomorph in the same genus Ajellomyces. In a phylogenic study of a wide range of ascomycete orders and families, Coccidioides immitis was found to be closest to Aphanoascus fulvescens and Chrysosporium keratinophilum, and to have relative distances to the remaining dimorphic genera (family Onygenaceae) similar to those of the dermatophytes (family Arthrodermataceae). The sequencing data were confirmed by genomic comparisons. All dimorphic genera had a nuclear DNA base composition in the same range of 46.6-47.3% G + C. The DNA melting curves of Blastomyces and Histoplasma strains showed irregularities that were ascribed to the presence of AT-rich stretches in satellite DNA rather than in mitochondrial DNA. Derivative profiles proved to be highly reproducible within regional populations and coincided with differences in clinical behaviour of each species. Blastomyces dermatitidis generated two kinds of curves, corresponding to the geographically distinct serotypes 1 and 2. The African type (serotype 2) was characterized by a classical sigmoidal melting curve similar to that for all strains of Coccidioides, Emmonsia and Paracoccidioides. In contrast, the American type (serotype 1) contained satellite DNA (27% G + C). A rRNA base difference of 1.5% was observed between geographical types, a value slightly higher than that noted between Histoplasma capsulatum and its variety farciminosum (0.9%). All three H. capsulatum varieties presented irregularities in their DNA melting curves. The molecular data support the recognition of two of them as agents of blastomycosis and the assignment of more than one species and two varieties to the genus Emmonsia.

Animals↗
PubMed2026

Is There a Fly in My Soup? To What Extent Do Metabarcoding and Individual Barcoding Tell the Same Story?

Metabarcoding has become the method of choice for characterizing complex arthropod communities. The extent to which metabarcoded bulk samples will recover the same community composition as individual sequencing of all individuals in the sample remains poorly quantified. Biases such as unequal extraction of DNA from different taxa, primer mismatches and non-random PCR may cause the selective drop-out of species from metabarcoding data. At the same time, DNA metabarcoding may reveal arthropod taxa present not as individuals, but as DNA residues on the surface or in the gut of insects. To quantify the consistency in sample contents established by different means, we metabarcoded 45 bulk insect samples, then extracted all arthropods and sequenced them individually. Metabarcoding targeted 418 bp at the 3' end of the Folmer barcoding region, while individual barcodes captured the entire 658 bp Folmer region. The metabarcoding workflow, including PCR amplification, sequencing and bioinformatics, was performed in three replicates from three separate lysate aliquots per sample. For the main analyses, sequences were assigned to Barcode Index Numbers (BINs) as identical taxonomic categories across data types, thereby allowing the detection of even rare but biologically true taxa. Since such reference-based validation will be unavailable to any researcher dealing with metabarcoding data alone, we validated our key findings through an alternative workflow, i.e., de novo clustering of sequences. We found that metabarcoding is replicable, as different replicates of the same sample recover similar species richness and composition. Individual barcoding and metabarcoding provide similar impressions of relative differences in community structure: species-rich vs. species-poor samples rank similarly among data types (Spearman's ⍴ = 0.88-0.99) as do differences in relative dissimilarity between sample pairs (Spearman's ⍴ = 0.55-0.90). Dissimilarity between data types varies with BIN richness in the sample, but this relationship reflects nestedness rather than turnover: metabarcoding recovers the same set of core species as individual barcoding but adds hundreds of species on top. Any BIN recovered as an individual occurred with high probability in the metabarcoding data, and any BIN found in high read abundances by metabarcoding was likely found as an individual (p > 0.8). In terms of abundances, the number of individual insects per BIN was well predicted by the number of metabarcoding reads (R2 > 0.68 for a model including taxonomy as a random effect). Our analysis suggests that metabarcoding data will be informative of the sample contents in terms of arthropod species richness, composition and taxon-specific abundances. Taxa recovered in low copy numbers in metabarcoding sequence data will likely represent DNA left as residues from past biotic interactions. Barring sequencing errors, both types of data yield biologically relevant insights into the taxa present in the source community.

Animals↗