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Draft genome sequence and detailed analysis of Pantoea eucrina strain Russ and implication for opportunistic pathogenesis

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ABSTRACT

The genus Pantoea is a predominant member of host-associated microbiome. We here report on the genomic analysis of Pantoea eucrina strain Russ that was isolated from a trashcan at Oklahoma State University, Stillwater, OK. The draft genome of Pantoea eucrina strain Russ consists of 3,939,877 bp of DNA with 3704 protein-coding genes and 134 RNA genes. This is the first report of a genome sequence of a member of Pantoea eucrina. Genomic analysis revealed metabolic versatility with genes involved in the metabolism and transport of all amino acids as well as glucose, fructose, mannose, xylose, arabinose and galactose, suggesting the organism is a versatile heterotroph. The genome also encodes an extensive secretory machinery including types I, II, III, IV, and Vb secretion systems, and several genes for pili production including the new usher/chaperone system (pfam 05,229). The implications of these systems for opportunistic pathogenesis are discussed.

No MeSH data available.


A maximum likelihood phylogenetic tree constructed using multiple sequence alignments of 16S rRNA genes. “Pantoea eucrina Russ” sequence is shown in bold. Reference sequences are also shown and Genbank accession numbers are given in parentheses. The tree was obtained under “K2 + G” model with a variable site γ shape parameter of 0.05. “Escherichia coli” was used as the out-group. Bootstrap values, in percent, are based on 100 replicates and are shown for branches with > 50% bootstrap support. Multiple sequence alignment, model selection, and maximum likelihood analysis were carried out in MEGA [28].
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f0010: A maximum likelihood phylogenetic tree constructed using multiple sequence alignments of 16S rRNA genes. “Pantoea eucrina Russ” sequence is shown in bold. Reference sequences are also shown and Genbank accession numbers are given in parentheses. The tree was obtained under “K2 + G” model with a variable site γ shape parameter of 0.05. “Escherichia coli” was used as the out-group. Bootstrap values, in percent, are based on 100 replicates and are shown for branches with > 50% bootstrap support. Multiple sequence alignment, model selection, and maximum likelihood analysis were carried out in MEGA [28].

Mentions: Within the genus Pantoea, 24 species are described with validly published names P. agglomerans type strain ATCC 27155T, P. allii type strain BD390T, P. ananatis type strain ATCC 33244T, P. anthophila type strain BD871T, P. brenneri type strain BD873T, P. calida type strain 1400/07T, P. citrea type strain BD875T, P. coffeiphila type strain DSM 28482T, P. conspicua type strain BD805T, P. cypripedii type strain ATCC 29267T, P. deleyi type strain BD767T, P. dispersa type strain ATCC 14589T, P. eucalypti type strain BD769T, P. eucrina type strain BD872T, P. gaviniae type strain A18/07T, P. intestinalis type strain DSM 28113T, P. punctata type strain BD876T, P. rodasii type strain BD943T, P. rwandensis type strain BD944T, P. septica type strain BD874T, P. stewartii type strain ATCC 8199T, P. terrea type strain BD877T, P. theicola type strain DSM 29212T, P. vagans type strain BD765T, and P. wallisii type strain BD946T. Strain Russ shares 96.6% with P. agglomerans, 96.3% P. allii, 97% P. ananatis, 97%P. anthophila, 96.6% P. brenneri, 96.4% P. calida, 94.9% P. citrea, 97.9% P. coffeiphila, 96.6% P. conspicua, 95.7% P. cypripedii, 96.8% P. deleyi, 98.5% P. dispersa, 96.4% P. eucalypti, 100% P. eucrina, 96.6% P. gaviniae, 95.5% P. intestinalis, 96.2% P. punctata, 97.5% P. rodasii, 97.5% P. rwandensis, 97.8% P. septica, 97.8% P. stewartii, 96.6% P. terrea, 96.3% P. theicola, 96.4% P. vagans, and 98.5% P. wallisii in the Pantoea genus. Phylogenetic analysis based on the 16S rRNA gene placed Pantoea eucrina strain Russ in the same node with the Pantoea eucrina strains IHB B 10086, C7, and CT194 (Table 2, and Fig. 2).


Draft genome sequence and detailed analysis of Pantoea eucrina strain Russ and implication for opportunistic pathogenesis
A maximum likelihood phylogenetic tree constructed using multiple sequence alignments of 16S rRNA genes. “Pantoea eucrina Russ” sequence is shown in bold. Reference sequences are also shown and Genbank accession numbers are given in parentheses. The tree was obtained under “K2 + G” model with a variable site γ shape parameter of 0.05. “Escherichia coli” was used as the out-group. Bootstrap values, in percent, are based on 100 replicates and are shown for branches with > 50% bootstrap support. Multiple sequence alignment, model selection, and maximum likelihood analysis were carried out in MEGA [28].
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC5037212&req=5

f0010: A maximum likelihood phylogenetic tree constructed using multiple sequence alignments of 16S rRNA genes. “Pantoea eucrina Russ” sequence is shown in bold. Reference sequences are also shown and Genbank accession numbers are given in parentheses. The tree was obtained under “K2 + G” model with a variable site γ shape parameter of 0.05. “Escherichia coli” was used as the out-group. Bootstrap values, in percent, are based on 100 replicates and are shown for branches with > 50% bootstrap support. Multiple sequence alignment, model selection, and maximum likelihood analysis were carried out in MEGA [28].
Mentions: Within the genus Pantoea, 24 species are described with validly published names P. agglomerans type strain ATCC 27155T, P. allii type strain BD390T, P. ananatis type strain ATCC 33244T, P. anthophila type strain BD871T, P. brenneri type strain BD873T, P. calida type strain 1400/07T, P. citrea type strain BD875T, P. coffeiphila type strain DSM 28482T, P. conspicua type strain BD805T, P. cypripedii type strain ATCC 29267T, P. deleyi type strain BD767T, P. dispersa type strain ATCC 14589T, P. eucalypti type strain BD769T, P. eucrina type strain BD872T, P. gaviniae type strain A18/07T, P. intestinalis type strain DSM 28113T, P. punctata type strain BD876T, P. rodasii type strain BD943T, P. rwandensis type strain BD944T, P. septica type strain BD874T, P. stewartii type strain ATCC 8199T, P. terrea type strain BD877T, P. theicola type strain DSM 29212T, P. vagans type strain BD765T, and P. wallisii type strain BD946T. Strain Russ shares 96.6% with P. agglomerans, 96.3% P. allii, 97% P. ananatis, 97%P. anthophila, 96.6% P. brenneri, 96.4% P. calida, 94.9% P. citrea, 97.9% P. coffeiphila, 96.6% P. conspicua, 95.7% P. cypripedii, 96.8% P. deleyi, 98.5% P. dispersa, 96.4% P. eucalypti, 100% P. eucrina, 96.6% P. gaviniae, 95.5% P. intestinalis, 96.2% P. punctata, 97.5% P. rodasii, 97.5% P. rwandensis, 97.8% P. septica, 97.8% P. stewartii, 96.6% P. terrea, 96.3% P. theicola, 96.4% P. vagans, and 98.5% P. wallisii in the Pantoea genus. Phylogenetic analysis based on the 16S rRNA gene placed Pantoea eucrina strain Russ in the same node with the Pantoea eucrina strains IHB B 10086, C7, and CT194 (Table 2, and Fig. 2).

View Article: PubMed Central - PubMed

ABSTRACT

The genus Pantoea is a predominant member of host-associated microbiome. We here report on the genomic analysis of Pantoea eucrina strain Russ that was isolated from a trashcan at Oklahoma State University, Stillwater, OK. The draft genome of Pantoea eucrina strain Russ consists of 3,939,877 bp of DNA with 3704 protein-coding genes and 134 RNA genes. This is the first report of a genome sequence of a member of Pantoea eucrina. Genomic analysis revealed metabolic versatility with genes involved in the metabolism and transport of all amino acids as well as glucose, fructose, mannose, xylose, arabinose and galactose, suggesting the organism is a versatile heterotroph. The genome also encodes an extensive secretory machinery including types I, II, III, IV, and Vb secretion systems, and several genes for pili production including the new usher/chaperone system (pfam 05,229). The implications of these systems for opportunistic pathogenesis are discussed.

No MeSH data available.