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| Status |
Public on Feb 12, 2015 |
| Title |
Whole transcriptome analysis of laser capture microdissected tissues reveals site-specific programming of the host epithelial transcriptome by the gut microbiota [short period of bacteria colonization] |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by array
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| Summary |
The mammalian gut harbors a diverse microbial community (gut microbiota) that mainly consists of bacteria. Their combined genomes (the microbiome) provide biochemical and metabolic functions that complement host physiology. Maintaining symbiosis seems to be a key requirement for health as dysbiosis is associated with the development of common diseases. Previous studies indicated that the microbiota and the host’s epithelium signal bidirectional inducing transcriptional responses to fine-tune and maintain symbiosis. However, little is known about the host’s responses to the microbiota along the length of the gut as earlier studies of gut microbial ecology mostly used either colonic or fecal samples. This is of importance as not only function and architecture of the gut varies along its length but also microbial distribution and diversity. Few recent studies have begun to investigate microbiota-induced host responses along the length of the gut. However, these reports used whole tissue samples and therefore do not allow drawing conclusions about specificity of the observed responses. Which cells in the intestinal tissue are responsible for the microbially induced response: epithelial, mesenchymal or immune cells? Where are the responding cells located? Furthermore, the gut microbiota has been implicated in epigenetic regulation of the host’s transcriptional profile.
We used using extensive microarray analysis of laser capture microdissection (LCM) harvested ileal and colonic tip and crypt fractions from germ-free mice before and during the time course of colonization with a normal microbiota (on days 1, 3, 5 and 7) to investigate the microbiota-induced transcriptional responses and their kinetics in specific and well-defined cell populations of the host’s epithelium.
Ileum and colon segments were dissected from germ-free 10-12 weeks old female C57Bl/6 mice and on day 1, 3, 5 and 7 after colonization, washed and frozen as OCT blocks. Cryosections were prepared from these OCT blocks and tip/crypt fractions isolated using laser capture microdissection.
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| Overall design |
To investigate the microbiota-induced transcriptional responses specific for specific subpopulations of intestinal epithelial cells and their kinetics, tip and crypt fractions of ileal and colonic epithelium of germ-free 10-12 weeks old female C57Bl/6 mice before and during the time course of colonization with a normal microbiota (on days 1, 3, 5 and 7) were harvested using laser capture microdissection and probed in an extensive microarray analysis.
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| Contributor(s) |
Sommer F, Nookaew I, Adam N, Fogelstrand P, Bäckhed F |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Oct 30, 2013 |
| Last update date |
Feb 21, 2018 |
| Contact name |
Intawat Nookaew |
| E-mail(s) |
inookaew@uams.edu
|
| Organization name |
University of Arkansas for Medical Sciences
|
| Department |
Department of Biomedical Informatics
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| Street address |
4301 W Markham St
|
| City |
Little Rock |
| ZIP/Postal code |
72205 |
| Country |
USA |
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| Platforms (1) |
| GPL16570 |
[MoGene-2_0-st] Affymetrix Mouse Gene 2.0 ST Array [transcript (gene) version] |
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| Samples (60)
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| This SubSeries is part of SuperSeries: |
| GSE51912 |
Whole transcriptome analysis of laser capture microdissected tissues reveals site-specific programming of the host epithelial transcriptome by the gut microbiota |
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| Relations |
| BioProject |
PRJNA225802 |
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