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Identification and characterisation of Pseudomonas 16S ribosomal DNA from ileal biopsies of children with Crohn's disease.

Wagner J, Short K, Catto-Smith AG, Cameron DJ, Bishop RF, Kirkwood CD - PLoS ONE (2008)

Bottom Line: Fifty eight percent of CD patients (18/32) were positive using the Pseudomonas PCR, while significantly fewer children in the non-IBD group, 33% (12/36), were PCR positive for Pseudomonas (p<0.05, Fischer's exact test).Pseudomonas species were less diverse in CD patients compared with non-IBD patients.In particular P.aeruginosa was only identified in non-IBD patients.

View Article: PubMed Central - PubMed

Affiliation: Enteric Virus Group, Murdoch Childrens Research Institute, Department of Paediatrics, Royal Children's Hospital, Parkville, Victoria, Australia.

ABSTRACT
Molecular analysis of bacterial 16S rRNA genes has made a significant contribution to the identification and characterisation of bacterial flora in the human gut. In particular, this methodology has helped characterise bacterial families implicated in the aetiology of inflammatory bowel disease (IBD). In this study we have used a genus specific bacterial 16S PCR to investigate the prevalence and diversity of Pseudomonas species derived from the ileum of children with Crohn's disease (CD), and from control children with non-inflammatory bowel disease (non-IBD) undergoing their initial endoscopic examination. Fifty eight percent of CD patients (18/32) were positive using the Pseudomonas PCR, while significantly fewer children in the non-IBD group, 33% (12/36), were PCR positive for Pseudomonas (p<0.05, Fischer's exact test). Pseudomonas specific 16S PCR products from 13 CD and 12 non-IBD children were cloned and sequenced. Five hundred and eighty one sequences were generated and used for the comparative analysis of Pseudomonas diversity between CD and non-IBD patients. Pseudomonas species were less diverse in CD patients compared with non-IBD patients. In particular P.aeruginosa was only identified in non-IBD patients.

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Related in: MedlinePlus

Phylogenetic tree generated from Pseudomonas type strains and consensus sequences from OTUs (OTU1-6) at sequence similarity threshold of 97%.Bootstrap values are base on 500 replications. The scale bar represents the nucleotide substitution per site. Underlined reference sequences are known human pathogenic strains. Shadowed box are considered as closely related species within each OTU group.
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pone-0003578-g002: Phylogenetic tree generated from Pseudomonas type strains and consensus sequences from OTUs (OTU1-6) at sequence similarity threshold of 97%.Bootstrap values are base on 500 replications. The scale bar represents the nucleotide substitution per site. Underlined reference sequences are known human pathogenic strains. Shadowed box are considered as closely related species within each OTU group.

Mentions: A consensus sequence of each of the 6 OTUs was generated, representing the 581 sequences determined from Pseudomonas 16S PCR products. Figure 2 shows the phylogenetic analysis of each OTU consensus sequences and sequences from 85 Pseudomonas reference strains. Each individual OTU clustered into distinct groups with specific Pseudomonas reference strains. OTU 1 grouped with P.migulae, P.proteolytica, P.brenneri, and P.panacis. OTU 2 grouped with P.mendocina, P.alcaliphila and P.pseudoalcaligenes. OTU 3 grouped P.mosselii, P.plecoglossicida and P.monteilii. OTU 4 grouped with P.fragi, P.lundensis, and P.psychrophila. OTU 5 formed a distinct group with P.nitroreducens and OTU 6 formed a distinct P.aeruginosa group.


Identification and characterisation of Pseudomonas 16S ribosomal DNA from ileal biopsies of children with Crohn's disease.

Wagner J, Short K, Catto-Smith AG, Cameron DJ, Bishop RF, Kirkwood CD - PLoS ONE (2008)

Phylogenetic tree generated from Pseudomonas type strains and consensus sequences from OTUs (OTU1-6) at sequence similarity threshold of 97%.Bootstrap values are base on 500 replications. The scale bar represents the nucleotide substitution per site. Underlined reference sequences are known human pathogenic strains. Shadowed box are considered as closely related species within each OTU group.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2572839&req=5

pone-0003578-g002: Phylogenetic tree generated from Pseudomonas type strains and consensus sequences from OTUs (OTU1-6) at sequence similarity threshold of 97%.Bootstrap values are base on 500 replications. The scale bar represents the nucleotide substitution per site. Underlined reference sequences are known human pathogenic strains. Shadowed box are considered as closely related species within each OTU group.
Mentions: A consensus sequence of each of the 6 OTUs was generated, representing the 581 sequences determined from Pseudomonas 16S PCR products. Figure 2 shows the phylogenetic analysis of each OTU consensus sequences and sequences from 85 Pseudomonas reference strains. Each individual OTU clustered into distinct groups with specific Pseudomonas reference strains. OTU 1 grouped with P.migulae, P.proteolytica, P.brenneri, and P.panacis. OTU 2 grouped with P.mendocina, P.alcaliphila and P.pseudoalcaligenes. OTU 3 grouped P.mosselii, P.plecoglossicida and P.monteilii. OTU 4 grouped with P.fragi, P.lundensis, and P.psychrophila. OTU 5 formed a distinct group with P.nitroreducens and OTU 6 formed a distinct P.aeruginosa group.

Bottom Line: Fifty eight percent of CD patients (18/32) were positive using the Pseudomonas PCR, while significantly fewer children in the non-IBD group, 33% (12/36), were PCR positive for Pseudomonas (p<0.05, Fischer's exact test).Pseudomonas species were less diverse in CD patients compared with non-IBD patients.In particular P.aeruginosa was only identified in non-IBD patients.

View Article: PubMed Central - PubMed

Affiliation: Enteric Virus Group, Murdoch Childrens Research Institute, Department of Paediatrics, Royal Children's Hospital, Parkville, Victoria, Australia.

ABSTRACT
Molecular analysis of bacterial 16S rRNA genes has made a significant contribution to the identification and characterisation of bacterial flora in the human gut. In particular, this methodology has helped characterise bacterial families implicated in the aetiology of inflammatory bowel disease (IBD). In this study we have used a genus specific bacterial 16S PCR to investigate the prevalence and diversity of Pseudomonas species derived from the ileum of children with Crohn's disease (CD), and from control children with non-inflammatory bowel disease (non-IBD) undergoing their initial endoscopic examination. Fifty eight percent of CD patients (18/32) were positive using the Pseudomonas PCR, while significantly fewer children in the non-IBD group, 33% (12/36), were PCR positive for Pseudomonas (p<0.05, Fischer's exact test). Pseudomonas specific 16S PCR products from 13 CD and 12 non-IBD children were cloned and sequenced. Five hundred and eighty one sequences were generated and used for the comparative analysis of Pseudomonas diversity between CD and non-IBD patients. Pseudomonas species were less diverse in CD patients compared with non-IBD patients. In particular P.aeruginosa was only identified in non-IBD patients.

Show MeSH
Related in: MedlinePlus