Recommended minimal standards for describing new species of the genus Helicobacter.

Dewhirst, Floyd E.; Fox, James G.; On, S. L. W.

doi:10.1099/00207713-50-6-2231

Cited by 85 publications

(78 citation statements)

References 29 publications

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“…Aerobic, endospore-forming bacteria (Logan et al, 2009) Anoxygenic phototrophic bacteria (Imhoff & Caumette, 2004) Genus Brucella (Corbel & Brinley Morgan, 1975a, b) Family Campylobacteraceae (Ursing et al, 1994) Family Flavobacteriaceae (Bernardet et al, 2002) Order Halobacteriales (Oren et al, 1997) Family Halomonadaceae (Arahal et al, 2007;Arahal et al, 2008) Genus Helicobacter (Dewhirst et al, 2000) Methanogenic bacteria (Archaea) (Boone & Whitman, 1988 (Bøvre & Henriksen, 1976) Genus Mycobacterium (Lévy-Frébault & Portaels, 1992) Family Pasteurellaceae (Christensen et al, 2007) Root and stem nodulating bacteria (Graham et al, 1991) Staphylococci (Freney et al, 1999) Genus Streptomyces (not a minimal standard, but a standard reference work, Shirling & Gottlieb, 1966) …”

Section: Minimal Standardsmentioning

confidence: 99%

Notes on the characterization of prokaryote strains for taxonomic purposes

Tindall

Rosselló‐Móra

Busse

et al. 2010

International Journal of Systematic and Evolutionary Microbiology

1,207

959

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Taxonomy relies on three key elements: characterization, classification and nomenclature. All three elements are dynamic fields, but each step depends on the one which precedes it. Thus, the nomenclature of a group of organisms depends on the way they are classified, and the classification (among other elements) depends on the information gathered as a result of characterization. While nomenclature is governed by the Bacteriological Code, the classification and characterization of prokaryotes is an area that is not formally regulated and one in which numerous changes have taken place in the last 50 years. The purpose of the present article is to outline the key elements in the way that prokaryotes are characterized, with a view to providing an overview of some of the pitfalls commonly encountered in taxonomic papers. INTRODUCTIONThe characterization of a strain is a key element in prokaryote systematics. Although various new methodologies have been developed over the past 100 years, both the newer methodologies and those considered to be 'traditional' remain key elements in determining whether a strain belongs to a known taxon or constitutes a novel one. In the case of a known taxon, a selected set of tests may be used to determine whether a strain has been identified as a member of an existing taxon. However, in the case of a strain or set of strains shown to be novel taxa, they should be characterized as comprehensively as possible. The goal of this characterization is to place them within the hierarchical framework laid down by the Bacteriological Code (1990 revision) (Lapage et al., 1992), as well as to provide a description of the taxa. Strains should be allocated to species (and/or subspecies), but the nature of the 'species name' (a binomial or combination) dictates that it must also be assigned to a genus. The genus may be either an existing or a novel genus. The Bacteriological Code also recommends that the placement of a genus in a family should be mentioned, and this can be extended to the other hierarchical levels as these become defined. Although this approach may appear novel, with much emphasis currently being placed on the species, the advent of 16S rRNA gene sequencing forces us to choose between primers that are specific for members of the Archaea or for members of the Bacteria, so the first step in that direction is already routine in many laboratories. However, such a classification system is only possible if strains are comprehensively and properly characterized. A further key element is the way in which datasets are compared and it is here too that some degree of guidance and a discussion of the potential problems needs to be provided. In the case of species, various recommendations have been made with respect to the ways in which species may be delineated and it is important to consider these aspects when considering how new strains are to be placed in novel species. However, far too little attention has been paid to the way in which taxa above the rank of species should be characterized a...

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Section: Minimal Standardsmentioning

confidence: 99%

Notes on the characterization of prokaryote strains for taxonomic purposes

Tindall

Rosselló‐Móra

Busse

et al. 2010

International Journal of Systematic and Evolutionary Microbiology

1,207

959

View full text Add to dashboard Cite

show abstract

“…Some Helicobacter species from diverse hosts may have zoonotic potential and have been associated with disease in both animals and humans. 3,5 Failure to isolate the Helicobacter species in the present report was not surprising given the standard methods utilized for diagnostic culture and the difficulties in isolating these fastidious organisms. 5 Molecular detection and characterization were very helpful in identifying the organism and provided a timely and relatively cost effective means of obtaining a diagnosis.…”

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confidence: 95%

Fatal Septicemia Caused by Helicobacter Infection in a Pancake Tortoise (Malacochersus Tornieri)

Stacy

Wellehan²

2010

J VET Diagn Invest

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Abstract. Bacteria of the genus Helicobacter are associated with disease in humans and animals. Reports of infection in reptiles are very limited. In the present study, pathological findings and molecular characterization are reported for a Helicobacter species associated with septicemia in a pancake tortoise (Malacochersus tornieri). Disseminated infection resulted in regional cellulitis and edema of the head and neck, and pericarditis. Spiral bacteria were identified in cytological preparations and Warthin-Starry-stained sections of pathological lesions. Amplification of partial sequence of the 16S ribosomal gene using polymerase chain reaction identified the organism as Helicobacter and suggest that it is a novel species.

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“…Biochemical and tolerance characteristics were carried out according to the recommendations of Dewhirst et al (2000). These data are reported in the species description presented below and a comparison of the most important phenotypic characteristics of the novel strains with those of other Helicobacter species is shown in Table 1.…”

mentioning

confidence: 99%

“…All isolates were identified as members of the genus Helicobacter using the genus-specific PCR described by Bohr et al (2002) and had identical physiological characteristics when examined as described by Dewhirst et al (2000) (Table 1).…”

mentioning

confidence: 99%

Helicobacter apri sp. nov., isolated from wild boars

Zanoni

Piva

Florio

et al. 2016

International Journal of Systematic and Evolutionary Microbiology

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Three isolates (A19 T , C21 and F12) with spiral-shaped cells and one bipolar sheathed flagellum were obtained from gastric mucosa and caecal contents of three different wild boars (Sus scrofa) and subjected to a polyphasic taxonomic study. A genus-specific PCR showed that these isolates belonged to the genus Helicobacter. Phylogenetic analysis based on 16S rRNA, 60-kDa heat-shock protein (HSP60) and atpA genes demonstrated they formed a novel lineage within this genus. Pairwise 16S rRNA, HSP60 and atpA gene sequence comparisons of the three isolates revealed 99.7, 99.4 and 99.9 % similarity, respectively, among the three isolates; the 16S rRNA gene of isolate A19 T shared 98.5 % sequence similarity with its nearest validly named neighbouring species, Helicobacter mastomyrinus (to the type strain MIT 97-5577 T ). The taxonomic uniqueness of the wild boar isolates was confirmed by protein analysis performed by matrix-assisted laser desorption/ionization time-of-flight MS and by a distinctive biochemical profile. These data indicated that isolates A19 T , C21 and F12 represent a novel taxon, for which the name Helicobacter apri sp. nov. is proposed, with isolate A19 T (=DSM 28990 T =LMG 28471 T ) as the type strain.The genus Helicobacter was erected by Goodwin (1989) with the description of two species: Helicobacter pylori and Helicobacter mustelae. Vandamme et al. (1991) transferred two additional Campylobacter species to this novel genus as Helicobacter fennelliae and Helicobacter cinaedi. The genus has since expanded considerably and, at the time of writing (October 2015), comprises 36 species with validly published names (Jeon et al., 2015), including several species isolated from the stomach of pigs and other animals (Dewhirst et al., 1994;Moyaert et al., 2007;Baele et al., 2008;Smet et al., 2012). In the present study, three novel isolates from three different animals, two recovered from caecal contents (A19 T and F12) and one from stomach mucosa (C21) of wild boars, were submitted to a polyphasic taxonomic characterization.From January to September 2011, during a study of gastric and intestinal Epsilonproteobacteria of wild boars killed within a programme for reducing their density in the Apennine Mountains in Bologna Province (Italy), Helicobacter isolates were obtained from 16 of 21 animals. In all 16 animals, Helicobacter isolates were recovered from caecal contents and in four animals they were also isolated from gastric mucosa. Isolations were made after 4 days of incubation at 37±1 C in a microaerobic atmosphere, on nutrient sheep-blood agar using a filter method (Zanoni et al., 2007) and, at the same time, on nutrient sheep-blood agar [Nutrient Broth No. 2 (Oxoid) with 1.5 % Bacto Agar (Difco) and 10 % sheep blood] plus Skirrow and Blaser Wang selective supplement (Oxoid). Agar plates were never more than 3-4Abbreviations: BI, Bayesian inference; MALDI-TOF, matrix-assisted laser desorption/ionization time-of-flight; ML, maximum-likelihood.

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Recommended minimal standards for describing new species of the genus Helicobacter.

Cited by 85 publications

References 29 publications

Notes on the characterization of prokaryote strains for taxonomic purposes

Notes on the characterization of prokaryote strains for taxonomic purposes

Fatal Septicemia Caused by Helicobacter Infection in a Pancake Tortoise (Malacochersus Tornieri)

Helicobacter apri sp. nov., isolated from wild boars

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