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Complete genome of the onion pathogen Enterobacter cloacae EcWSU1.

Humann JL, Wildung M, Cheng CH, Lee T, Stewart JE, Drew JC, Triplett EW, Main D, Schroeder BK - Stand Genomic Sci (2011)

View Article: PubMed Central - PubMed

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Previous studies have shown that the members of the Enterobacter cloacae complex are difficult to differentiate with biochemical tests and in phylogenetic studies using multilocus sequence analysis, strains of the same species separate into numerous clusters... Enterobacter cloacae is ubiquitous in nature and is known to cause disease in numerous plants, such as onion, ginger, papaya, and macadamia... In addition, E. cloacae is an emerging opportunistic human pathogen that is associated with nosocomial infections... Interestingly, E. cloacae strains separate into six clusters indicating considerable diversity within the species... In addition, many new strains are identified as E. cloacae due to traditional phenotype tests and 16S rRNA identity, but when other regions of the genome, or the genome as a whole, are compared, they appear to have more differences within a species than observed between species of other genera of bacteria [, Humann and Schroeder, unpublished]... The genome sequence reported here will allow for comparisons on a genome-wide level with other E. cloacae strains and may help clarify the relationships between the E. cloacae complex members as well as allow for identification of putative pathogenesis genes... Cronobacter sakazakii BAA-894, formerly Enterobacter sakazakii, clustered with E. cloacae subsp. cloacae NCTC 9394 (0.90 posterior probability), which was isolated from human feces... Interestingly, all the E. cloacae strains did not cluster together... The genome sequence of E. cloacae subsp. cloacae ATCC 13047 (CP001918) initially was used as a reference sequence for assembly of the pyrosequencing reads... However, the genomic sequence of EcWSU1 did not have sufficient identity to the DNA sequence of ATCC 13047 for this to be effective (only 19.56% of the reads mapped to ATCC 13047)... As a result, the EcWSU1 genome was closed by developing primers that amplified out from each end of the contigs... Genome annotation was completed using the Bacterial Annotation System (BASys). tRNA sequences were determined using tRNAscan-SE and rRNA sequences were identified by searching the genome sequence with rRNA sequences from E. cloacae subsp. cloacae ATCC 13047 using a private nucleotide BLAST server... The numbers of genes assigned to each COG functional category are listed in Table 4... About one sixth (15.3%) of the annotated genes were not assigned to a COG or have an unknown function.

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Phylogenetic tree of 16S rRNA sequences from strains of Enterobacter with genome sequences. Bayesian phylogenetic analyses of the 16S rRNA region yielded two distinct clusters, supported with a 0.90 posterior probability. Analyses were implemented in MRBAYES [24]. The Bayesian Information Criterion (BIC), DT-ModSel [25] was used to determine the nucleotide substitution model best suited for the dataset. The Markov chain Monte Carlo search included two runs with four chains each for 1,000,000 generations, ensuring that the average split frequencies between the runs was less than 1%. Pectobacterium served as the outgroup for the analysis. Numbers in parentheses behind the bacterial names correspond to the Genbank accession numbers for the genome sequences. The scale bar indicates the number of substitutions/site.
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f1: Phylogenetic tree of 16S rRNA sequences from strains of Enterobacter with genome sequences. Bayesian phylogenetic analyses of the 16S rRNA region yielded two distinct clusters, supported with a 0.90 posterior probability. Analyses were implemented in MRBAYES [24]. The Bayesian Information Criterion (BIC), DT-ModSel [25] was used to determine the nucleotide substitution model best suited for the dataset. The Markov chain Monte Carlo search included two runs with four chains each for 1,000,000 generations, ensuring that the average split frequencies between the runs was less than 1%. Pectobacterium served as the outgroup for the analysis. Numbers in parentheses behind the bacterial names correspond to the Genbank accession numbers for the genome sequences. The scale bar indicates the number of substitutions/site.

Mentions: E. cloacae EcWSU1 was isolated from onion bulbs that were exhibiting symptoms of rot [8]. EcWSU1 is a Gram-negative, rod shaped bacterium of the family “Enterobacteriaceae” (Table 1). Species differentiation of the Enterobacter genus is difficult with biochemical and phylogenetic tests [6]. The genetic complexity of the E. cloacae complex is illustrated in a phylogenetic tree of the 16S rRNA region (Figure 1). EcWSU1 grouped with the type-strain E. cloacae subsp. cloacae ATCC 13047 with a 0.71 posterior probability in a Bayesian phylogenetic analysis. E. cloacae SCF1, isolated from soil in Puerto Rico, grouped closely with Enterobacter sp. 638 [26], an endophyte of poplar trees. Cronobacter sakazakii BAA-894, formerly Enterobacter sakazakii [27], clustered with E. cloacae subsp. cloacae NCTC 9394 (0.90 posterior probability), which was isolated from human feces. Interestingly, all the E. cloacae strains did not cluster together.


Complete genome of the onion pathogen Enterobacter cloacae EcWSU1.

Humann JL, Wildung M, Cheng CH, Lee T, Stewart JE, Drew JC, Triplett EW, Main D, Schroeder BK - Stand Genomic Sci (2011)

Phylogenetic tree of 16S rRNA sequences from strains of Enterobacter with genome sequences. Bayesian phylogenetic analyses of the 16S rRNA region yielded two distinct clusters, supported with a 0.90 posterior probability. Analyses were implemented in MRBAYES [24]. The Bayesian Information Criterion (BIC), DT-ModSel [25] was used to determine the nucleotide substitution model best suited for the dataset. The Markov chain Monte Carlo search included two runs with four chains each for 1,000,000 generations, ensuring that the average split frequencies between the runs was less than 1%. Pectobacterium served as the outgroup for the analysis. Numbers in parentheses behind the bacterial names correspond to the Genbank accession numbers for the genome sequences. The scale bar indicates the number of substitutions/site.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3368419&req=5

f1: Phylogenetic tree of 16S rRNA sequences from strains of Enterobacter with genome sequences. Bayesian phylogenetic analyses of the 16S rRNA region yielded two distinct clusters, supported with a 0.90 posterior probability. Analyses were implemented in MRBAYES [24]. The Bayesian Information Criterion (BIC), DT-ModSel [25] was used to determine the nucleotide substitution model best suited for the dataset. The Markov chain Monte Carlo search included two runs with four chains each for 1,000,000 generations, ensuring that the average split frequencies between the runs was less than 1%. Pectobacterium served as the outgroup for the analysis. Numbers in parentheses behind the bacterial names correspond to the Genbank accession numbers for the genome sequences. The scale bar indicates the number of substitutions/site.
Mentions: E. cloacae EcWSU1 was isolated from onion bulbs that were exhibiting symptoms of rot [8]. EcWSU1 is a Gram-negative, rod shaped bacterium of the family “Enterobacteriaceae” (Table 1). Species differentiation of the Enterobacter genus is difficult with biochemical and phylogenetic tests [6]. The genetic complexity of the E. cloacae complex is illustrated in a phylogenetic tree of the 16S rRNA region (Figure 1). EcWSU1 grouped with the type-strain E. cloacae subsp. cloacae ATCC 13047 with a 0.71 posterior probability in a Bayesian phylogenetic analysis. E. cloacae SCF1, isolated from soil in Puerto Rico, grouped closely with Enterobacter sp. 638 [26], an endophyte of poplar trees. Cronobacter sakazakii BAA-894, formerly Enterobacter sakazakii [27], clustered with E. cloacae subsp. cloacae NCTC 9394 (0.90 posterior probability), which was isolated from human feces. Interestingly, all the E. cloacae strains did not cluster together.

View Article: PubMed Central - PubMed

AUTOMATICALLY GENERATED EXCERPT
Please rate it.

Previous studies have shown that the members of the Enterobacter cloacae complex are difficult to differentiate with biochemical tests and in phylogenetic studies using multilocus sequence analysis, strains of the same species separate into numerous clusters... Enterobacter cloacae is ubiquitous in nature and is known to cause disease in numerous plants, such as onion, ginger, papaya, and macadamia... In addition, E. cloacae is an emerging opportunistic human pathogen that is associated with nosocomial infections... Interestingly, E. cloacae strains separate into six clusters indicating considerable diversity within the species... In addition, many new strains are identified as E. cloacae due to traditional phenotype tests and 16S rRNA identity, but when other regions of the genome, or the genome as a whole, are compared, they appear to have more differences within a species than observed between species of other genera of bacteria [, Humann and Schroeder, unpublished]... The genome sequence reported here will allow for comparisons on a genome-wide level with other E. cloacae strains and may help clarify the relationships between the E. cloacae complex members as well as allow for identification of putative pathogenesis genes... Cronobacter sakazakii BAA-894, formerly Enterobacter sakazakii, clustered with E. cloacae subsp. cloacae NCTC 9394 (0.90 posterior probability), which was isolated from human feces... Interestingly, all the E. cloacae strains did not cluster together... The genome sequence of E. cloacae subsp. cloacae ATCC 13047 (CP001918) initially was used as a reference sequence for assembly of the pyrosequencing reads... However, the genomic sequence of EcWSU1 did not have sufficient identity to the DNA sequence of ATCC 13047 for this to be effective (only 19.56% of the reads mapped to ATCC 13047)... As a result, the EcWSU1 genome was closed by developing primers that amplified out from each end of the contigs... Genome annotation was completed using the Bacterial Annotation System (BASys). tRNA sequences were determined using tRNAscan-SE and rRNA sequences were identified by searching the genome sequence with rRNA sequences from E. cloacae subsp. cloacae ATCC 13047 using a private nucleotide BLAST server... The numbers of genes assigned to each COG functional category are listed in Table 4... About one sixth (15.3%) of the annotated genes were not assigned to a COG or have an unknown function.

No MeSH data available.