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Defining the microbial transcriptional response to colitis through integrated host and microbiome profiling
Nicholas Edward Ilott1, Julia Bollrath1,2, Camille Danne1
1Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK.
The ISME Journal
|March 23, 2016
Summary
Inflammatory bowel diseases alter the gut microbiome. This study reveals microbial adaptations to inflammatory stressors, driven by host immune responses and oxidative stress, impacting bacterial gene expression.
Area of Science:
- Microbiology
- Immunology
- Gastroenterology
Background:
- Inflammatory bowel diseases (IBD) are associated with significant gut microbiome alterations.
- The precise mechanisms driving these microbial shifts in IBD remain incompletely understood.
Purpose of the Study:
- To investigate changes in gut microbiome structure and transcriptional activity in a mouse model of colitis.
- To characterize the relationship between host and microbial transcriptional responses during intestinal inflammation.
Main Methods:
- Combined metagenomic and metatranscriptomic profiling of the gut microbiome.
- Transcriptomic analysis of colonic tissue and luminal RNA.
- Analysis of host immune cell transcriptional signatures.
Main Results:
- Colitis induced increased abundance and transcription of microbial genes related to nutrient deprivation, antimicrobial peptide resistance, and oxidative stress.
- Host transcriptional analysis revealed activated macrophages and granulocytes, including calprotectin (S100a8/S100a9) expression.
- Microbial genes for oxidative stress resistance showed greater transcriptional changes than DNA abundance changes, suggesting environmental stressor influence.
Conclusions:
- Commensal microbes adapt to the inflammatory environment in colitis by altering gene expression to cope with stressors.
- Host immune responses, particularly oxidative stress, play a significant role in shaping the microbial transcriptional landscape during IBD.
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