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Metagenomic Characterization of Microbial Communities In Situ Within the Deeper Layers of the Ileum in Crohn’s Disease
BACKGROUND & AIMS: Microbial dysbiosis and aberrant host–microbe interactions in the gut are believed to contribute to the development and progression of Crohn’s disease (CD). Microbiome studies in CD typically have focused on microbiota in feces or superficial mucosal layers of the colon becaus...
Autores principales: | , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5042890/ https://www.ncbi.nlm.nih.gov/pubmed/28174737 http://dx.doi.org/10.1016/j.jcmgh.2016.05.011 |
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author | Pedamallu, Chandra Sekhar Bhatt, Ami S. Bullman, Susan Fowler, Sharyle Freeman, Samuel S. Durand, Jacqueline Jung, Joonil Duke, Fujiko Manzo, Veronica Cai, Diana Ananthakrishnan, Ashwin Ojesina, Akinyemi I. Ramachandran, Aruna Gevers, Dirk Xavier, Ramnik J. Bhan, Atul K. Meyerson, Matthew Yajnik, Vijay |
author_facet | Pedamallu, Chandra Sekhar Bhatt, Ami S. Bullman, Susan Fowler, Sharyle Freeman, Samuel S. Durand, Jacqueline Jung, Joonil Duke, Fujiko Manzo, Veronica Cai, Diana Ananthakrishnan, Ashwin Ojesina, Akinyemi I. Ramachandran, Aruna Gevers, Dirk Xavier, Ramnik J. Bhan, Atul K. Meyerson, Matthew Yajnik, Vijay |
author_sort | Pedamallu, Chandra Sekhar |
collection | PubMed |
description | BACKGROUND & AIMS: Microbial dysbiosis and aberrant host–microbe interactions in the gut are believed to contribute to the development and progression of Crohn’s disease (CD). Microbiome studies in CD typically have focused on microbiota in feces or superficial mucosal layers of the colon because accessing DNA from deeper layers of the bowel is challenging. In this study, we analyzed the deep tissue microbiome in patients who underwent surgical resection of the small intestine. METHODS: Paraffin blocks were obtained from 12 CD patients undergoing ileocecal resection, and healthy ileum samples (inflammatory bowel disease–free controls) were obtained from 12 patients undergoing surgery for right-sided colon cancer. Diseased and healthy-appearing ileum was identified using microscopy, and paraffin blocks were macrodissected using a core needle to specifically isolate DNA. Illumina Whole Genome Sequencing was used for microbial sequence identification and subsequent taxonomic classification using the PathSeq tool. RESULTS: We observed significant differences between the microbiome of CD samples vs inflammatory bowel disease–free controls, including depletion of Bacteroidetes and Clostridia. Notably, microbial composition at the phyla level did not differ markedly between healthy and diseased areas of CD patients. However, we observed enrichment of potentially pathogenic organisms at the species level. CONCLUSIONS: Our study showed dysbiosis within deeper layers of the ileum of CD patients, specifically enrichment of enterotoxigenic Staphylococcus aureus and an environmental Mycobacterium species not described previously. Future studies with larger cohort sizes are warranted to confirm these findings. Studies would benefit from effective microbial DNA extraction methods from paraffin sections and host nucleic acid depletion approaches to increase microbial read coverage. |
format | Online Article Text |
id | pubmed-5042890 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
spelling | pubmed-50428902017-02-07 Metagenomic Characterization of Microbial Communities In Situ Within the Deeper Layers of the Ileum in Crohn’s Disease Pedamallu, Chandra Sekhar Bhatt, Ami S. Bullman, Susan Fowler, Sharyle Freeman, Samuel S. Durand, Jacqueline Jung, Joonil Duke, Fujiko Manzo, Veronica Cai, Diana Ananthakrishnan, Ashwin Ojesina, Akinyemi I. Ramachandran, Aruna Gevers, Dirk Xavier, Ramnik J. Bhan, Atul K. Meyerson, Matthew Yajnik, Vijay Cell Mol Gastroenterol Hepatol Brief Report BACKGROUND & AIMS: Microbial dysbiosis and aberrant host–microbe interactions in the gut are believed to contribute to the development and progression of Crohn’s disease (CD). Microbiome studies in CD typically have focused on microbiota in feces or superficial mucosal layers of the colon because accessing DNA from deeper layers of the bowel is challenging. In this study, we analyzed the deep tissue microbiome in patients who underwent surgical resection of the small intestine. METHODS: Paraffin blocks were obtained from 12 CD patients undergoing ileocecal resection, and healthy ileum samples (inflammatory bowel disease–free controls) were obtained from 12 patients undergoing surgery for right-sided colon cancer. Diseased and healthy-appearing ileum was identified using microscopy, and paraffin blocks were macrodissected using a core needle to specifically isolate DNA. Illumina Whole Genome Sequencing was used for microbial sequence identification and subsequent taxonomic classification using the PathSeq tool. RESULTS: We observed significant differences between the microbiome of CD samples vs inflammatory bowel disease–free controls, including depletion of Bacteroidetes and Clostridia. Notably, microbial composition at the phyla level did not differ markedly between healthy and diseased areas of CD patients. However, we observed enrichment of potentially pathogenic organisms at the species level. CONCLUSIONS: Our study showed dysbiosis within deeper layers of the ileum of CD patients, specifically enrichment of enterotoxigenic Staphylococcus aureus and an environmental Mycobacterium species not described previously. Future studies with larger cohort sizes are warranted to confirm these findings. Studies would benefit from effective microbial DNA extraction methods from paraffin sections and host nucleic acid depletion approaches to increase microbial read coverage. Elsevier 2016-05-26 /pmc/articles/PMC5042890/ /pubmed/28174737 http://dx.doi.org/10.1016/j.jcmgh.2016.05.011 Text en © 2016 The Authors http://creativecommons.org/licenses/by-nc-nd/4.0/ This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). |
spellingShingle | Brief Report Pedamallu, Chandra Sekhar Bhatt, Ami S. Bullman, Susan Fowler, Sharyle Freeman, Samuel S. Durand, Jacqueline Jung, Joonil Duke, Fujiko Manzo, Veronica Cai, Diana Ananthakrishnan, Ashwin Ojesina, Akinyemi I. Ramachandran, Aruna Gevers, Dirk Xavier, Ramnik J. Bhan, Atul K. Meyerson, Matthew Yajnik, Vijay Metagenomic Characterization of Microbial Communities In Situ Within the Deeper Layers of the Ileum in Crohn’s Disease |
title | Metagenomic Characterization of Microbial Communities In Situ Within the Deeper Layers of the Ileum in Crohn’s Disease |
title_full | Metagenomic Characterization of Microbial Communities In Situ Within the Deeper Layers of the Ileum in Crohn’s Disease |
title_fullStr | Metagenomic Characterization of Microbial Communities In Situ Within the Deeper Layers of the Ileum in Crohn’s Disease |
title_full_unstemmed | Metagenomic Characterization of Microbial Communities In Situ Within the Deeper Layers of the Ileum in Crohn’s Disease |
title_short | Metagenomic Characterization of Microbial Communities In Situ Within the Deeper Layers of the Ileum in Crohn’s Disease |
title_sort | metagenomic characterization of microbial communities in situ within the deeper layers of the ileum in crohn’s disease |
topic | Brief Report |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5042890/ https://www.ncbi.nlm.nih.gov/pubmed/28174737 http://dx.doi.org/10.1016/j.jcmgh.2016.05.011 |
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