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Pedamallu CS, Bhatt AS, Bullman S, Fowler S, Freeman SS, Durand J, Jung J, Duke F, Manzo V, Cai D, Ananthakrishnan A, Ojesina AI, Ramachandran A, Gevers D, Xavier RJ, Bhan AK, Meyerson M, Yajnik V. Metagenomic Characterization of Microbial Communities In Situ Within the Deeper Layers of the Ileum in Crohn's Disease. Cell Mol Gastroenterol Hepatol 2016; 2:563-566.e5. [PMID: 28174737 PMCID: PMC5042890 DOI: 10.1016/j.jcmgh.2016.05.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 05/15/2016] [Indexed: 01/26/2023]
Abstract
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.
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Affiliation(s)
- Chandra Sekhar Pedamallu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts,Broad Institute of MIT and Harvard, Cambridge, Massachusetts,Harvard Medical School, Boston, Massachusetts
| | - Ami S. Bhatt
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Susan Bullman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Sharyle Fowler
- Crohn’s and Colitis Center, Massachusetts General Hospital, Boston, Massachusetts
| | | | - Jacqueline Durand
- Crohn’s and Colitis Center, Massachusetts General Hospital, Boston, Massachusetts
| | - Joonil Jung
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Fujiko Duke
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Veronica Manzo
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Diana Cai
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | - Akinyemi I. Ojesina
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Aruna Ramachandran
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Dirk Gevers
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Ramnik J. Xavier
- Crohn’s and Colitis Center, Massachusetts General Hospital, Boston, Massachusetts
| | - Atul K. Bhan
- Crohn’s and Colitis Center, Massachusetts General Hospital, Boston, Massachusetts,Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts,Broad Institute of MIT and Harvard, Cambridge, Massachusetts,Harvard Medical School, Boston, Massachusetts,Matthew Meyerson, MD, PhD, Dana-Farber Cancer Institute, Boston, Massachusetts 02215. fax: 617-582-7880.Dana-Farber Cancer InstituteBostonMassachusetts 02215
| | - Vijay Yajnik
- Crohn’s and Colitis Center, Massachusetts General Hospital, Boston, Massachusetts,Correspondence Address correspondence to: Vijay Yajnik, MD, PhD, Crohn's and Colitis Center, Massachusetts General Hospital, Massachusetts 02114.Crohn's and Colitis CenterMassachusetts General HospitalMassachusetts 02114
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