Immune Gene Expression Covaries with Gut Microbiome Composition in Stickleback

Area of Science:

• Microbiology and Immunology
• Genomics and Bioinformatics
• Aquatic Ecology and Vertebrate Physiology

Background:

• Commensal microbial communities significantly influence vertebrate host physiology and fitness.
• Host immunity is closely tied to gut microbiota composition via complex, poorly understood bidirectional interactions.
• Host gene expression is a potential mediator of these microbiota-host functional links.

Purpose of the Study:

• To investigate correlations between gut microbiome composition and host immune gene expression in a nonmammalian vertebrate.
• To explore the relationship between microbial diversity, specific microbial taxa abundance, and immune gene expression in three-spined stickleback (Gasterosteus aculeatus).

Main Methods:

• Analysis of gene expression in the head kidney of laboratory-raised three-spined stickleback.
• Correlation analysis between microbiome alpha diversity and host immune gene expression.
• Correlation analysis between the abundance of specific microbial families and host gene expression.

Main Results:

• Significant positive associations were found between microbial alpha diversity and the expression of host immune genes.
• Fifteen microbial families showed strong correlations with host gene expression, categorized by positive, negative, or neutral relationships with immune processes.
• Specific immune processes, including macrophage and B cell functions, were commonly associated with the abundance of these correlated microbial taxa.

Conclusions:

• The study supports hypotheses linking host immunity and gut microbiome composition in vertebrates.
• Microbiome composition, including diversity and specific taxa, is correlated with immune gene expression in a systemic manner, affecting organs distant from the gut.
• Findings advance the understanding of immune-microbiome interactions in natural, non-model systems.