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Microbial Population Differentials between Mucosal and Submucosal Intestinal Tissues in Advanced Crohn's Disease of the Ileum.

Chiodini RJ, Dowd SE, Chamberlin WM, Galandiuk S, Davis B, Glassing A - PLoS ONE (2015)

Bottom Line: A variety of organisms of the Phylum Firmicutes were increased in the subjacent submucosa as compared to the parallel mucosal tissue including Ruminococcus spp., Oscillospira spp., Pseudobutyrivibrio spp., and Tumebacillus spp.In addition, Propionibacterium spp. and Cloacibacterium spp. were increased as well as large increases in Proteobacteria including Parasutterella spp. and Methylobacterium spp.Our data demonstrate the existence of a distinct submucosal microbiome and ecosystem that is not well reflected in the mucosa and/or downstream fecal material.

View Article: PubMed Central - PubMed

Affiliation: St. Vincent Healthcare, Sisters of Charity of Leavenworth Health System, Billings, Montana, United States of America; Department of Biological and Physical Sciences, Montana State University-Billings, Billings, Montana, United States of America.

ABSTRACT
Since Crohn's disease is a transmural disease, we hypothesized that examination of deep submucosal tissues directly involved in the inflammatory disease process may provide unique insights into bacterial populations transgressing intestinal barriers and bacterial populations more representative of the causes and agents of the disease. We performed deep 16s microbiota sequencing on isolated ilea mucosal and submucosal tissues on 20 patients with Crohn's disease and 15 non-inflammatory bowel disease controls with a depth of coverage averaging 81,500 sequences in each of the 70 DNA samples yielding an overall resolution down to 0.0001% of the bacterial population. Of the 4,802,328 total sequences generated, 98.9% or 4,749,183 sequences aligned with the Kingdom Bacteria that clustered into 8545 unique sequences with <3% divergence or operational taxonomic units enabling the identification of 401 genera and 698 tentative bacterial species. There were significant differences in all taxonomic levels between the submucosal microbiota in Crohn's disease compared to controls, including organisms of the Order Desulfovibrionales that were present within the submucosal tissues of most Crohn's disease patients but absent in the control group. A variety of organisms of the Phylum Firmicutes were increased in the subjacent submucosa as compared to the parallel mucosal tissue including Ruminococcus spp., Oscillospira spp., Pseudobutyrivibrio spp., and Tumebacillus spp. In addition, Propionibacterium spp. and Cloacibacterium spp. were increased as well as large increases in Proteobacteria including Parasutterella spp. and Methylobacterium spp. This is the first study to examine the microbial populations within submucosal tissues of patients with Crohn's disease and to compare microbial communities found deep within the submucosal tissues with those present on mucosal surfaces. Our data demonstrate the existence of a distinct submucosal microbiome and ecosystem that is not well reflected in the mucosa and/or downstream fecal material.

No MeSH data available.


Related in: MedlinePlus

Influence and effect of rRNA gene copy number on the relative abundance of bacterial populations.Conversion of data to relative percent of population based on the number of 16s rRNA operons in each organism, thereby representing the number of bacteria or genomes, had a major effect on the composition of the bacterial communities within the mucosa and submucosa. Certain bacteria are either over or under represented when a 1:1 ratio is assumed per normal bioinformatics. Similar disparities were found at all bacterial divisions. Legend: Fasta Count: Relative abundance based on the assumption that each rRNA sequence alignment is equivalent to a single bacterial genome/cell as used in most bioinformatics analyses. rrn Operon Count: relative bacterial abundance based on the average number of rRNA operons in each bacterial cell (fasta count/rrn operons) thereby more accurately reflecting bacterial prevalence.
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pone.0134382.g002: Influence and effect of rRNA gene copy number on the relative abundance of bacterial populations.Conversion of data to relative percent of population based on the number of 16s rRNA operons in each organism, thereby representing the number of bacteria or genomes, had a major effect on the composition of the bacterial communities within the mucosa and submucosa. Certain bacteria are either over or under represented when a 1:1 ratio is assumed per normal bioinformatics. Similar disparities were found at all bacterial divisions. Legend: Fasta Count: Relative abundance based on the assumption that each rRNA sequence alignment is equivalent to a single bacterial genome/cell as used in most bioinformatics analyses. rrn Operon Count: relative bacterial abundance based on the average number of rRNA operons in each bacterial cell (fasta count/rrn operons) thereby more accurately reflecting bacterial prevalence.

Mentions: Re-calibration of bacterial frequencies within tissue populations based on the actual number of 16s rRNA operons, and hence more closely correlating with actual bacterial counts, resulted in significant changes in the relative frequencies of the microbial populations within tissues and altered the relative composition of the microbiota (Fig 2).


Microbial Population Differentials between Mucosal and Submucosal Intestinal Tissues in Advanced Crohn's Disease of the Ileum.

Chiodini RJ, Dowd SE, Chamberlin WM, Galandiuk S, Davis B, Glassing A - PLoS ONE (2015)

Influence and effect of rRNA gene copy number on the relative abundance of bacterial populations.Conversion of data to relative percent of population based on the number of 16s rRNA operons in each organism, thereby representing the number of bacteria or genomes, had a major effect on the composition of the bacterial communities within the mucosa and submucosa. Certain bacteria are either over or under represented when a 1:1 ratio is assumed per normal bioinformatics. Similar disparities were found at all bacterial divisions. Legend: Fasta Count: Relative abundance based on the assumption that each rRNA sequence alignment is equivalent to a single bacterial genome/cell as used in most bioinformatics analyses. rrn Operon Count: relative bacterial abundance based on the average number of rRNA operons in each bacterial cell (fasta count/rrn operons) thereby more accurately reflecting bacterial prevalence.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4519195&req=5

pone.0134382.g002: Influence and effect of rRNA gene copy number on the relative abundance of bacterial populations.Conversion of data to relative percent of population based on the number of 16s rRNA operons in each organism, thereby representing the number of bacteria or genomes, had a major effect on the composition of the bacterial communities within the mucosa and submucosa. Certain bacteria are either over or under represented when a 1:1 ratio is assumed per normal bioinformatics. Similar disparities were found at all bacterial divisions. Legend: Fasta Count: Relative abundance based on the assumption that each rRNA sequence alignment is equivalent to a single bacterial genome/cell as used in most bioinformatics analyses. rrn Operon Count: relative bacterial abundance based on the average number of rRNA operons in each bacterial cell (fasta count/rrn operons) thereby more accurately reflecting bacterial prevalence.
Mentions: Re-calibration of bacterial frequencies within tissue populations based on the actual number of 16s rRNA operons, and hence more closely correlating with actual bacterial counts, resulted in significant changes in the relative frequencies of the microbial populations within tissues and altered the relative composition of the microbiota (Fig 2).

Bottom Line: A variety of organisms of the Phylum Firmicutes were increased in the subjacent submucosa as compared to the parallel mucosal tissue including Ruminococcus spp., Oscillospira spp., Pseudobutyrivibrio spp., and Tumebacillus spp.In addition, Propionibacterium spp. and Cloacibacterium spp. were increased as well as large increases in Proteobacteria including Parasutterella spp. and Methylobacterium spp.Our data demonstrate the existence of a distinct submucosal microbiome and ecosystem that is not well reflected in the mucosa and/or downstream fecal material.

View Article: PubMed Central - PubMed

Affiliation: St. Vincent Healthcare, Sisters of Charity of Leavenworth Health System, Billings, Montana, United States of America; Department of Biological and Physical Sciences, Montana State University-Billings, Billings, Montana, United States of America.

ABSTRACT
Since Crohn's disease is a transmural disease, we hypothesized that examination of deep submucosal tissues directly involved in the inflammatory disease process may provide unique insights into bacterial populations transgressing intestinal barriers and bacterial populations more representative of the causes and agents of the disease. We performed deep 16s microbiota sequencing on isolated ilea mucosal and submucosal tissues on 20 patients with Crohn's disease and 15 non-inflammatory bowel disease controls with a depth of coverage averaging 81,500 sequences in each of the 70 DNA samples yielding an overall resolution down to 0.0001% of the bacterial population. Of the 4,802,328 total sequences generated, 98.9% or 4,749,183 sequences aligned with the Kingdom Bacteria that clustered into 8545 unique sequences with <3% divergence or operational taxonomic units enabling the identification of 401 genera and 698 tentative bacterial species. There were significant differences in all taxonomic levels between the submucosal microbiota in Crohn's disease compared to controls, including organisms of the Order Desulfovibrionales that were present within the submucosal tissues of most Crohn's disease patients but absent in the control group. A variety of organisms of the Phylum Firmicutes were increased in the subjacent submucosa as compared to the parallel mucosal tissue including Ruminococcus spp., Oscillospira spp., Pseudobutyrivibrio spp., and Tumebacillus spp. In addition, Propionibacterium spp. and Cloacibacterium spp. were increased as well as large increases in Proteobacteria including Parasutterella spp. and Methylobacterium spp. This is the first study to examine the microbial populations within submucosal tissues of patients with Crohn's disease and to compare microbial communities found deep within the submucosal tissues with those present on mucosal surfaces. Our data demonstrate the existence of a distinct submucosal microbiome and ecosystem that is not well reflected in the mucosa and/or downstream fecal material.

No MeSH data available.


Related in: MedlinePlus