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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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Diversity analysis of Pseudomonas 16S ribosomal sequences obtained from Crohn's disease patients and non-inflammatory bowel disease control patients.Five hundred and eighty one sequences from the Crohn's disease (CD) and non-inflammatory bowel disease (non-IBD) patient libraries were grouped into operational taxonomic units (OTU) using a sequence similarity threshold of 97%. The fraction of sequences in each OTU and patient group were calculated and presented. * Significant more sequences in these OTUs compared to the other patient group (p<0.01, Fisher exact test).
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pone-0003578-g001: Diversity analysis of Pseudomonas 16S ribosomal sequences obtained from Crohn's disease patients and non-inflammatory bowel disease control patients.Five hundred and eighty one sequences from the Crohn's disease (CD) and non-inflammatory bowel disease (non-IBD) patient libraries were grouped into operational taxonomic units (OTU) using a sequence similarity threshold of 97%. The fraction of sequences in each OTU and patient group were calculated and presented. * Significant more sequences in these OTUs compared to the other patient group (p<0.01, Fisher exact test).

Mentions: All 581 sequences from the P16S gene library were organised into operational taxonomic units (OTU) using DOTUR. Each OTU consists of a group of P16S sequences with 97% sequence similarity. The P16S sequences were grouped into 6 OTUs of which five were identified in the CD clone library and all six in the non-IBD clone library (supporting table S3). Five OTUs were common to both clone libraries. One OTU was unique to the non-IBD clone library. The majority of sequences (67.2% CD and 43.3% non-IBD) were found in the OTU 1. The second most commonly identified sequences were found in OTU 2 (18.8% CD and 13% non-IBD). OTU 3 sequences were present in 11.3% of the CD group and in 8.4% of the non-IBD group. OTU 4 represented 10% of sequences in the non-IBD group whilst this OTU was only a minor fraction within the CD group (0.6%). OTU 5 sequences were only identified in the non-IBD group (18%). OTU 6 was the least common type, identified in 7.3% of non-IBD and 2.2% of CD sequences (Figure 1). The number of sequences in each individual OTU was tested against the number of sequences in the remaining OTUs between the two patient groups using Fischer's exact test. A significant difference was identified in OTU 1 and OTUs 4, 5, and 6 between CD and non-IBD patient groups (p<0.01) (Figure 1 marked with *).


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)

Diversity analysis of Pseudomonas 16S ribosomal sequences obtained from Crohn's disease patients and non-inflammatory bowel disease control patients.Five hundred and eighty one sequences from the Crohn's disease (CD) and non-inflammatory bowel disease (non-IBD) patient libraries were grouped into operational taxonomic units (OTU) using a sequence similarity threshold of 97%. The fraction of sequences in each OTU and patient group were calculated and presented. * Significant more sequences in these OTUs compared to the other patient group (p<0.01, Fisher exact test).
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2572839&req=5

pone-0003578-g001: Diversity analysis of Pseudomonas 16S ribosomal sequences obtained from Crohn's disease patients and non-inflammatory bowel disease control patients.Five hundred and eighty one sequences from the Crohn's disease (CD) and non-inflammatory bowel disease (non-IBD) patient libraries were grouped into operational taxonomic units (OTU) using a sequence similarity threshold of 97%. The fraction of sequences in each OTU and patient group were calculated and presented. * Significant more sequences in these OTUs compared to the other patient group (p<0.01, Fisher exact test).
Mentions: All 581 sequences from the P16S gene library were organised into operational taxonomic units (OTU) using DOTUR. Each OTU consists of a group of P16S sequences with 97% sequence similarity. The P16S sequences were grouped into 6 OTUs of which five were identified in the CD clone library and all six in the non-IBD clone library (supporting table S3). Five OTUs were common to both clone libraries. One OTU was unique to the non-IBD clone library. The majority of sequences (67.2% CD and 43.3% non-IBD) were found in the OTU 1. The second most commonly identified sequences were found in OTU 2 (18.8% CD and 13% non-IBD). OTU 3 sequences were present in 11.3% of the CD group and in 8.4% of the non-IBD group. OTU 4 represented 10% of sequences in the non-IBD group whilst this OTU was only a minor fraction within the CD group (0.6%). OTU 5 sequences were only identified in the non-IBD group (18%). OTU 6 was the least common type, identified in 7.3% of non-IBD and 2.2% of CD sequences (Figure 1). The number of sequences in each individual OTU was tested against the number of sequences in the remaining OTUs between the two patient groups using Fischer's exact test. A significant difference was identified in OTU 1 and OTUs 4, 5, and 6 between CD and non-IBD patient groups (p<0.01) (Figure 1 marked with *).

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