Metagenomic Characterization of Microbial CommunitiesIn SituWithin the Deeper Layers of the Ileum in Crohn's Disease.
OBJECTIVE
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 thePathSeqtool.


RESULTS
We observed significant differences between the microbiome of CD samples vs inflammatory bowel disease-free controls, including depletion ofBacteroidetesandClostridia. 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 enterotoxigenicStaphylococcus aureusand an environmentalMycobacteriumspecies 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.
Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts; Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Harvard Medical School, Boston, Massachusetts.
Chandra Sekhar
CS
Pedamallu
Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts; Broad Institute of MIT and Harvard, Cambridge, Massachusetts.
Ami S
AS
Bhatt
Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts; Broad Institute of MIT and Harvard, Cambridge, Massachusetts.
Susan
S
Bullman
Crohn's and Colitis Center, Massachusetts General Hospital, Boston, Massachusetts.
Sharyle
S
Fowler
Broad Institute of MIT and Harvard, Cambridge, Massachusetts.
Samuel S
SS
Freeman
Crohn's and Colitis Center, Massachusetts General Hospital, Boston, Massachusetts.
Jacqueline
J
Durand
Broad Institute of MIT and Harvard, Cambridge, Massachusetts.
Joonil
J
Jung
Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts; Broad Institute of MIT and Harvard, Cambridge, Massachusetts.
Fujiko
F
Duke
Broad Institute of MIT and Harvard, Cambridge, Massachusetts.
Veronica
V
Manzo
Broad Institute of MIT and Harvard, Cambridge, Massachusetts.
Diana
D
Cai
Crohn's and Colitis Center, Massachusetts General Hospital, Boston, Massachusetts.
Ashwin
A
Ananthakrishnan
Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts; Broad Institute of MIT and Harvard, Cambridge, Massachusetts.
Akinyemi I
AI
Ojesina
Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts; Broad Institute of MIT and Harvard, Cambridge, Massachusetts.
Aruna
A
Ramachandran
Broad Institute of MIT and Harvard, Cambridge, Massachusetts.
Dirk
D
Gevers
Crohn's and Colitis Center, Massachusetts General Hospital, Boston, Massachusetts.
Ramnik J
RJ
Xavier
Crohn's and Colitis Center, Massachusetts General Hospital, Boston, Massachusetts; Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts.
Atul K
AK
Bhan
Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts; Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Harvard Medical School, Boston, Massachusetts.
Matthew
M
Meyerson
Crohn's and Colitis Center, Massachusetts General Hospital, Boston, Massachusetts.
Vijay
V
Yajnik
CD, Crohn's disease; Crohn's Disease; Deeper Mucosal Layers; FDR, false-discovery rate; IBD, inflammatory bowel disease; LDA, linear discriminant analysis; Microbial Dysbiosis