Is 16S rDNA a Reliable Phylogenetic Marker to Characterize Relationships Below the Family Level in the Enterobacteriaceae?

Naum, Marianna; Brown, Eric W.; Mason‐Gamer, Roberta J.

doi:10.1007/s00239-008-9115-3

Cited by 101 publications

(78 citation statements)

References 27 publications

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“…However, bootstrap values for each clade were low, indicating that the phylogenetic position of strain QC88-366 T was not certain. This kind of phenomenon has been reported previously, where several genera within Enterobacteriaceae were shown to be polyphyletic based on 16S rRNA gene sequence phylogeny (Naum et al, 2008;Popp et al, 2010). Therefore, it was difficult to classify the isolate systematically on the basis of 16S rRNA gene sequences, as it was close to the borderline among multiple genera within Enterobacteriaceae.…”

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confidence: 72%

Pantoea theicola sp. nov., isolated from black tea

Tanaka¹,

Horie²,

Mochida³

et al. 2015

International Journal of Systematic and Evolutionary Microbiology

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A Gram-negative, facultatively anaerobic strain was isolated from black tea. On the basis of 16S rRNA gene sequence similarity comparisons, strain QC88-366 T was grouped into the genus Pantoea, being related most closely to the type strains of Pantoea gaviniae (98.5 %) and Pantoea calida (98.3 %); sequence similarities were #97.0 % to the type strains of other species of the genus Pantoea. Multilocus sequence analysis based on partial sequences of the gyrB, rpoB, infB and atpD genes also revealed P. gaviniae and P. calida as the closest phylogenetic relatives. The fatty acid profile showed the major fatty acids of strain QC88-366 T were C 16 : 0 , C 16 : 1 and C 18 : 1 , the same as those of its closest related species. However, the ratio of C 16 : 1 , C 17 : 0 cyclo, C 18 : 1 and C 18 : 2 differed slightly compared with those of the related neighbours. In addition, the results of physiological and biochemical tests also allowed the phenotypic differentiation of strain QC88-366 T from its closest phylogenetic neighbours. The G+C content of the DNA was 57.2 mol%. Strain QC88-366 T therefore represents a novel species of the genus Pantoea, for which the name Pantoea theicola sp. nov. is proposed. The type strain is QC88-366 T (5DSM 29212 T 5NBRC 110557 T ).In food hygiene management, bacteria of the family Enterobacteriaceae have been used as indicators to judge possible contamination and inadequate sterilization of food products. In particular, their presence in non-sterilized or pasteurized foods, for example powdered infant formula and milk, indicates a potential risk of food poisoning by pathogenic enteric bacteria. It is a requirement that some commercial additives to pasteurized food show no presence of Enterobacteriaceae. During our investigation of the microbial flora associated with black tea leaves, strain QC88-366 T was isolated as a surviving Enterobacteriaceae after heat treatment sterilization. The result of partial 59 end 16S rRNA gene sequence analysis showed that strain QC88-366 T was related to the family Enterobacteriaceae, but it could not be identified to the species level. This study deals with the further characterization of strain QC88-366 T and shows that it represents a novel species of the genus Pantoea.Strain QC88-366 T was obtained from black tea extract heated at 90 8C for 12 min. The tea extract was suspended in sterilized water, inoculated in mTGC medium (Nissui) and incubated under anaerobic conditions for 48 h at 35 8C. The culture was then plated on plate count agar (PCA; Merck) and incubated for 24 h at 35 8C. A single colony was picked up and streaked onto a PCA plate, and the pure culture was preliminarily identified based on 59 end partial 16S rRNA gene sequencing analysis using a MicroSeq 500 bacterial identification kit (Life Technologies). Thus, strain QC88-366 T was obtained and initial analysis indicated that it belonged to the family Enterobacteriaceae. Reference type strains of related Enterobacteriaceae were obtained from the Belgian Coordinated Collections of Microor...

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confidence: 72%

Pantoea theicola sp. nov., isolated from black tea

Tanaka¹,

Horie²,

Mochida³

et al. 2015

International Journal of Systematic and Evolutionary Microbiology

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“…In that study, strains from DNA HG II, IV and V (referred to as MLSA groups E, F, H and I) and Pectobacterium cypripedii were suggested to be members of the genus Pantoea. Previous studies have also questioned the taxonomic position of Pectobacterium cypripedii, as it does not cluster with other Pectobacterium species and several different 16S rRNA gene sequences are available for the type strain of this species (Spröer et al, 1999;Samson et al, 2005;Young & Park, 2007;Naum et al, 2008;Yarza et al, 2008). In this study, we propose the taxonomic reclassification of strains from Brenner's DNA HG II, IV and V and Pectobacterium cypripedii within the genus Pantoea.…”

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confidence: 72%

Emended description of the genus Pantoea, description of four species from human clinical samples, Pantoea septica sp. nov., Pantoea eucrina sp. nov., Pantoea brenneri sp. nov. and Pantoea conspicua sp. nov., and transfer of Pectobacterium cypripedii (Hori 1911) Brenner et al. 1973 emend. Hauben et al. 1998 to the genus as Pantoea cypripedii comb. nov.

Brady

Cleenwerck

Venter

et al. 2010

International Journal of Systematic and Evolutionary Microbiology

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Bacterial strains belonging to DNA hybridization groups (HG) II, IV and V, in the Erwinia herbicola-Enterobacter agglomerans complex, of Brenner et al. [Int J Syst Bacteriol 34 (1984), [45][46][47][48][49][50][51][52][53][54][55] were suggested previously to belong to the genus Pantoea, but have never been formally described and classified. Additionally, it has been shown in several studies that Pectobacterium cypripedii is more closely related to species of Pantoea than to those of Pectobacterium. In this study, the phylogenetic positions of Brenner's DNA HG II, IV and V and Pectobacterium cypripedii were re-examined by both 16S rRNA gene sequencing and multilocus sequence analyses (MLSA) based on the gyrB, rpoB, atpD and infB genes. The analyses revealed that DNA HG II, IV and V and Pectobacterium cypripedii form five separate branches within the genus Pantoea (strains from HG V were split into two branches). DNA-DNA hybridization data further confirmed that DNA HG II, IV and V constitute four separate species. Pectobacterium cypripedii was shown to be a close phylogenetic relative of Pantoea dispersa and DNA HG IV by both 16S rRNA gene sequence and MLSA analyses. Biochemical analyses performed on strains from DNA HG II, IV and V and Pectobacterium cypripedii confirmed their taxonomic position within the genus Pantoea and revealed phenotypic characteristics that allow the differentiation of these species from each other and from their closest phylogenetic neighbours. It is proposed to emend the description of the genus Pantoea and to describe Pantoea septica sp. nov. for DNA HG II (type strain LMG 5345 T 5BD 874 T 5CDC 3123-70 T ), Pantoea eucrina sp. nov. for DNA HG IV (type strain LMG 2781 T 5BD 872 T 5CDC 1741-71 T 5LMG 5346 T ), Pantoea brenneri sp. nov. for strains of DNA HG V excluding LMG 24534 (type strain LMG 5343 T 5BD 873 T 5CDC 3482-71 T ) and Pantoea conspicua sp. nov. for the remaining strain of DNA HG V (type strain LMG 24534 T 5BD 805 T 5CDC 3527-71 T ) and to transfer Pectobacterium cypripedii to the genus as Pantoea cypripedii comb. nov. (type strain LMG 2657 T 5ATCC 29267 T 5DSM 3873 T 5LMG 2655 T ).Abbreviations: HG, hybridization group; MLSA, multilocus sequence analysis.

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“…Strains of Erwinia, Brenneria, Pectobacterium, Dickeya and Pantoea were obtained from the American Type Culture Collection (ATCC), United States Department of Agriculture (USDA) (Appalachian Fruit Research Center, Kearneysville, WV), and from Dr Amy Charkowski (University of Wisconsin, Madison) as frozen cultures and LuriaBertani (LB) slants respectively. Sample authentication was confirmed based on 16S rDNA sequence analysis prior to their use (Naum et al, 2008).…”

Section: Methodsmentioning

confidence: 99%

“…This economically important group of enterobacterial plant pathogens is distributed worldwide, and they vary widely in their ecology, host range tropism, and pathogenicity (Krieg & Holt, 1985). The strains used in this study have been well characterized taxonomically and their evolutionary history has been described based on numerous housekeeping genes (Brown et al, 2000;Hauben et al, 1998;Naum et al, 2008;Young & Park, 2007). For example, Fig.…”

Section: Introductionmentioning

confidence: 99%

“…For example, Fig. 2(a) depicts a de novo evolutionary reconstruction of enterobacterial plant pathogenic species based on 16S rDNA gene sequences (Naum et al, 2008). To understand the role of horizontal gene transfer (HGT) of T3SS genes among the enterobacterial plant pathogens, we analysed sequences from four genes, hrcC, hrcR, hrcJ and hrcV.…”

Section: Introductionmentioning

confidence: 99%

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Phylogenetic evidence for extensive horizontal gene transfer of type III secretion system genes among enterobacterial plant pathogens

2009

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This study uses sequences from four genes, which are involved in the formation of the type III secretion apparatus, to determine the role of horizontal gene transfer in the evolution of virulence genes for the enterobacterial plant pathogens. Sequences of Erwinia, Brenneria, Pectobacterium, Dickeya and Pantoea were compared (a) with one another, (b) with sequences of enterobacterial animal pathogens, and (c) with sequences of plant pathogenic c and b proteobacteria, to evaluate probable paths of lateral exchange leading to the current distribution of virulence determinants among these micro-organisms. Phylogenies were reconstructed based on hrcC, hrcR, hrcJ and hrcV gene sequences using parsimony and maximum-likelihood algorithms. Virulence gene phylogenies were also compared with several housekeeping gene loci in order to evaluate patterns of lateral versus vertical acquisition. The resulting phylogenies suggest that multiple horizontal gene transfer events have occurred both within and among the enterobacterial plant pathogens and plant pathogenic c and b proteobacteria. hrcJ sequences are the most similar, exhibiting anywhere from 2 to 50 % variation at the nucleotide level, with the highest degree of variation present between plant and animal pathogen sequences. hrcV sequences are conserved among plant and animal pathogens at the N terminus. The C-terminal domain is conserved only among the enterobacterial plant pathogens, as are the hrcC and hrcR sequences. Additionally, hrcJ and hrcV sequence phylogenies suggest that at least some type III secretion system virulence genes from enterobacterial plant pathogens are related more closely to those of the genus Pseudomonas, a conclusion neither supported nor refuted by hrcC or hrcR.

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Is 16S rDNA a Reliable Phylogenetic Marker to Characterize Relationships Below the Family Level in the Enterobacteriaceae?

Cited by 101 publications

References 27 publications

Pantoea theicola sp. nov., isolated from black tea

Pantoea theicola sp. nov., isolated from black tea

Phylogenetic evidence for extensive horizontal gene transfer of type III secretion system genes among enterobacterial plant pathogens

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