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| Status |
Public on Jul 01, 2017 |
| Title |
Patterns of host gene expression associated with harboring a foregut microbial community |
| Organisms |
Rattus norvegicus; Neotoma stephensi |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We compared gene expression in the foregut tissues of two rodent species: Stephen's woodrat (Neotoma stephensi), which harbors a dense foregut microbial community, and the lab rat (Rattus norvegicus), which lacks such a community. We found that woodrats have higher abundances of transcripts associated with smooth muscle processes, specifically a higher expression of the smoothelin-like 1 gene, which may assist in contractile properties of this tissue to retain food material in the foregut chamber. The expression of genes associated with keratinization and cornification exhibited a complex pattern of differences between the two species, suggesting distinct molecular mechanisms for this process in each of the two species. Lab rats exhibited higher abundances of transcripts associated with immune function, likely to inhibit microbial growth in the foregut of this species. Some of our results were consistent with previous findings in ruminants (high expression of facilitative glucose transporters, lower expression of B4galnt2), suggestive of possible convergent evolution, while other results were unclear, and perhaps represent novel host-microbe interactions in rodents. Overall, our results suggest that harboring a foregut microbiota is associated with changes to the functions and host-microbe interactions of the foregut tissues.
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| Overall design |
Foregut tissue, polyA-containing mRNA profiles of Stephens' woodrats (Neotoma stephensi) and Sprague Dawley lab rats generated by deep sequencing, in triplicate, using the Illumina HiSeq 2000 platform.
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| Contributor(s) |
Weiss RB, Kohl KD, Dearing MD |
| Citation(s) |
28874116 |
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| Submission date |
Jul 13, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Robert B Weiss |
| E-mail(s) |
bob.weiss@genetics.utah.edu
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| Phone |
(801) 585-5606
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| Organization name |
University of Utah
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| Department |
Human Genetics
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| Lab |
EIHG, Rm 2260B
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| Street address |
15 N 2030 E
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| City |
Salt Lake City |
| State/province |
UT |
| ZIP/Postal code |
84112 |
| Country |
USA |
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| Platforms (2) |
| GPL14844 |
Illumina HiSeq 2000 (Rattus norvegicus) |
| GPL22154 |
Illumina HiSeq 2000 (Neotoma stephensi) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA329014 |
| SRA |
SRP078462 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE84381_RAW.tar |
950.0 Kb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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