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Regulation of Host Gene Expression by Gastrointestinal Tract Microbiota in Chinook Salmon (Oncorhynchus tshawytscha)
  • Javad Sadeghi,
  • Subba Rao Chaganti,
  • Daniel Heath
Javad Sadeghi
University of Windsor

Corresponding Author:[email protected]

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Subba Rao Chaganti
University of Michigan
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Daniel Heath
University of Windsor
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Abstract

Differences in gut microbiome composition are linked with health, disease and ultimately host fitness; however, the molecular mechanisms underlying that relationship are not well characterized. Here, we modified the fish gut microbiota using antibiotic and probiotic feed treatments to address the effect of host microbiome on gene expression patterns. Chinook salmon (Oncorhynchus tshawytscha) gut gene expression was evaluated using whole transcriptome sequencing (RNA-Seq) on hindgut mucosa samples from individuals treated with antibiotic, probiotic and control diets to determine differentially expressed (DE) host genes. Fifty DE host genes were selected for further characterization using nanofluidic qPCR chips. We used 16S rRNA gene metabarcoding to characterize the rearing water and host gut microbiome bacterial communities. Daily administration of antibiotics and probiotics resulted in significant changes in fish gut and aquatic microbiota as well as more than 100 DE genes in the antibiotic and probiotic treatment fish, relative to healthy controls. Normal microbiota depletion by antibiotics mostly led to downregulation of different aspects of immunity and upregulation of apoptotic process. In the probiotic treatment, genes related to post-translation modification and inflammatory responses were up-regulated relative to controls. Our qPCR results revealed significant effects of treatment (antibiotic and probiotic) on rabep2, aifm3, manf, prmt3 gene transcription. Moreover, we found significant associations between members of Lactobacillaceae and Aeromonadaceae with host gene expression patterns. Overall, our analysis showed that the microbiota had significant impacts on many host signaling pathways, specifically targeting immune, developmental, and metabolic processes. Our characterization of some of the molecular mechanisms involved in microbiome-host interactions will help develop new strategies for preventing/ treating microbiome disruption-related diseases.
31 Aug 2022Submitted to Molecular Ecology
01 Sep 2022Submission Checks Completed
01 Sep 2022Assigned to Editor
11 Oct 2022Reviewer(s) Assigned
02 Mar 2023Review(s) Completed, Editorial Evaluation Pending
21 Mar 2023Editorial Decision: Revise Minor
27 Apr 20231st Revision Received
04 May 2023Submission Checks Completed
04 May 2023Assigned to Editor
04 May 2023Review(s) Completed, Editorial Evaluation Pending
05 May 2023Reviewer(s) Assigned
25 May 2023Editorial Decision: Accept