Polyphasic taxonomy, a consensus approach to bacterial systematics.

Vandamme, Peter; Pot, Bruno; Gillis, Monique; Vos, Paul De; Kersters, Karel; Swings, Jean

doi:10.1128/mmbr.60.2.407-438.1996

Cited by 1,026 publications

(524 citation statements)

References 254 publications

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“…SDS-PAGE of cellular and extracellular components can give rise to highly discriminatory typing methods, with applications in taxonomy also [16,[131][132][133][134]. In the 1980s, these methods were applied to a variety of organisms, but since the 1990s they have been largely superseded by DNA-based methods.…”

Section: Phenotypic Typing Methodsmentioning

confidence: 99%

Guidelines for the validation and application of typing methods for use in bacterial epidemiology

Belkum

Tassios

Dijkshoorn

et al. 2007

Clinical Microbiology and Infection

678

516

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For bacterial typing to be useful, the development, validation and appropriate application of typing methods must follow unified criteria. Over a decade ago, ESGEM, the ESCMID (Europen Society for Clinical Microbiology and Infectious Diseases) Study Group on Epidemiological Markers, produced guidelines for optimal use and quality assessment of the then most frequently used typing procedures. We present here an update of these guidelines, taking into account the spectacular increase in the number and quality of typing methods made available over the past decade. Newer and older, phenotypic and genotypic methods for typing of all clinically relevant bacterial species are described according to their principles, advantages and disadvantages. Criteria for their evaluation and application and the interpretation of their results are proposed. Finally, the issues of reporting, standardisation, quality assessment and international networks are discussed. It must be emphasised that typing results can never stand alone and need to be interpreted in the context of all available epidemiological, clinical and demographical data relating to the infectious disease under investigation. A strategic effort on the part of all workers in the field is thus mandatory to combat emerging infectious diseases, as is financial support from national and international granting bodies and health authorities.

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Section: Phenotypic Typing Methodsmentioning

confidence: 99%

Guidelines for the validation and application of typing methods for use in bacterial epidemiology

Belkum

Tassios

Dijkshoorn

et al. 2007

Clinical Microbiology and Infection

678

516

View full text Add to dashboard Cite

show abstract

“…For statistical analysis, sequences sharing more than 97% sequence identity were considered as a single phylotype (Vandamme et al, 1996). The clone coverage was calculated according with the following equation: C = 1 À (n/N), where n is the number of singleton phylotypes, and N is the total number of clones screened in the clone library (Good, 1953).…”

Section: Estimation Of the Size Of The Clone Librariesmentioning

confidence: 99%

Microbial diversity in bovine papillomatous digital dermatitis in Holstein dairy cows from upstate New York

Santos

Pereira

Caixeta

et al. 2011

FEMS Microbiol Ecol

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Papillomatous digital dermatitis (PDD) is one of the most prevalent diseases of cattle, adversely affecting the dairy industry by its negative effect on milk production and reproductive performance. Our objective was to use culture-independent methods to determine the microbial diversity in different strata of PDD lesions of three Holstein dairy cows, analyzing whether major differences exist compared to foot skin of three non-infected cows. Both group-specific 16S rRNA gene PCR-denaturing gradient gel electrophoresis and clone library sequencing of broad-range 16S rRNA gene showed differences between the microbial composition of healthy dairy cows and the different strata of the lesion. The predominant bacterial community in the lesion, regardless of the stratum, consisted of 166 specific phylotypes belonging to seven bacterial phyla. Spirochetes (particularly, treponemes) was the most prominent group detected in PDD deep biopsies and was only found in samples from the lesion. Additionally, one phylotype phylogenetically affiliated with uncultured Euryarchaeota was detected in two strata of the lesion. Sequences from healthy foot skin samples revealed 86 specific phylotypes that were affiliated with Firmicutes and Proteobacteria. Our study corroborates the theory that treponemes are involved in PDD disease etiology and suggests, for the first time, the presence of archaeal members in this particular bovine infection.

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“…The genus-speci®c probe S-G-Dtm-0229-a-A-18 targets a phylogenetic branch of organisms with 16S rDNA sequence similarities of between 89% and 93% (Stackebrandt et al, 1997). This level of similarity is commonly found within subclasses or families rather than within genera (Vandamme et al, 1996). Thus, while probe S-G-Dtm-0229-a-A-18 is genus speci®c based on the valid taxonomy of Desulfotomaculum, this probe is more likely to be family speci®c for the`Desulfotomaculaceae' (although this family is not yet de®ned).…”

Section: Characterization Of Environmental Samplesmentioning

confidence: 99%

Desulfotomaculum genus‐ and subgenus‐specific 16S rRNA hybridization probes for environmental studies

Hristova¹,

Mau²,

Zheng³

et al. 2000

Environmental Microbiology

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Based on comparative analysis of 16S rRNA sequences and the recently established phylogeny of the genus Desulfotomaculum, a set of phylogenetically nested hybridization probes was developed and characterized. A genus-specific probe targets all known Desulfotomaculum species (with the exception of Desulfotomaculum acetoxidans), and five specific probes target subclusters within the Desulfotomaculum genus. The dissociation temperature of each probe was determined experimentally. Probe specificities were verified through hybridizations with pure culture rRNA isolated from a wide variety of target and non-target organisms and through an evaluation of probe 'nesting' using samples obtained from four different environments. Fixation and hybridization conditions for fluorescence in situ hybridizations were also optimized. The probes were used in quantitative membrane hybridizations to determine the abundance of Desulfotomaculum species in thermophilic anaerobic digesters, in soil, in human faeces and in pig colon samples. Desulfotomaculum rRNA accounted for 0.3-2.1% of the total rRNA in the digesters, 2.6-6.6% in soil, 1.5-3.3% in human faeces and 2.5-6.2% in pig colon samples.

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Polyphasic taxonomy, a consensus approach to bacterial systematics.

Cited by 1,026 publications

References 254 publications

Guidelines for the validation and application of typing methods for use in bacterial epidemiology

Guidelines for the validation and application of typing methods for use in bacterial epidemiology

Microbial diversity in bovine papillomatous digital dermatitis in Holstein dairy cows from upstate New York

Desulfotomaculum genus‐ and subgenus‐specific 16S rRNA hybridization probes for environmental studies

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