Regulation of Host Gene Expression by Gastrointestinal Tract Microbiota
in Chinook Salmon (Oncorhynchus tshawytscha)
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.