Authors: Javad Sadeghi, Subba Rao Chaganti, Daniel Heath
The fish gut microbiome holds complex communities of resident microorganisms, linked with health, disease and ultimately host fitness, yet little is known how the gut microbiota influences and is influenced by host gene expression. Here, we modified the gut microbiota in juvenile Chinook salmon using antibiotic and probiotic feed treatments and used transcriptome sequencing, 16S bacterial metabarcoding, and OpenArray Taqman quantitative PCR (STP Chip) approaches to address the effect of changes in the host microbiome on host gut gene expression patterns. Daily administration of antibiotics and probiotics resulted in significant changes in the fish gut and tank water microbiomes and resulted in more than 100 differentially expressed host genes in the antibiotic and probiotic groups, relative to healthy controls. The hindgut of probiotic treatment group was vastly dominated by Lactobacillaceae and Bifidobacteriaceae, but these families were much less abundant in the antibiotic and control groups. Normal bacterial depletion by antibiotic treatment led to downregulation of immune-related genes with an upregulation of apoptotic processes. The fish that received the probiotic treatment exhibited upregulation of post-translation modification and inflammatory response genes, relative to the control treatment. Our OpenArray Taqman qPCR analyses showed similar patterns of response. Moreover, two probiotics bacteria taxa (Lactobacillaceae and Bifidobacteriaceae) showed significant correlation with host gene expression patterns. Overall, our analyses showed that the gut microbiota had significant impacts on host gut tissue signalling pathways, particularly affecting immune, developmental and metabolic responses. Our characterization of some of the molecular mechanisms involved in microbiome-host interactions will help develop new strategies for using gut microbiome manipulation for preventing/treating microbiome disruption-related diseases in captive-reared fish.
