New Publication: Host-Microbe Interactions Shape Gene Expression in Stickleback

Groundbreaking publication in Genome Biology and Evolution reveals asymmetric contributions of host genetics and microbiota to gene expression!

Clay Small, Kathryn Milligan-Myhre, Susan Bassham, Karen Guillemin, and Bill Cresko demonstrate subtle but significant genotype-by-environment interactions between host genetics and the microbiota, affecting expression of genes involved in immunity, coagulation, focal adhesion, and metabolism.

Major Discovery

The research reveals:

• Asymmetric contributions to transcriptional variation
• Host genotype effects dominate overall
• Microbiota influences specific pathways
• G×E interactions shape immune responses
• Complex host-microbe dialogue

Transcriptomic Innovation

Key findings include:

• RNA-seq analysis of gnotobiotic fish
• Pathway-specific expression patterns
• Statistical G×E interactions
• Systems-level understanding
• Novel analytical approaches

Affected Pathways

Microbiota influences:

• Innate immunity responses
• Coagulation cascades
• Complement system
• Focal adhesion pathways
• Cancer-related genes
• Peroxisome function

Gnotobiotic Excellence

This work showcases:

• Controlled microbiome experiments
• Germ-free fish technology
• Precise colonization protocols
• Host-microbe systems biology
• Model organism advantages

Evolutionary Implications

Findings suggest:

• Co-evolution of host and microbes
• Population-specific adaptations
• Microbiome’s role in local adaptation
• Genetic variation in microbe response
• Evolutionary potential of holobiont

Methodological Advances

The study employed:

• Gnotobiotic experimental design
• High-throughput RNA sequencing
• Advanced statistical modeling
• Pathway enrichment analysis
• G×E interaction detection

Biomedical Relevance

Applications include:

• Understanding microbiome health effects
• Personalized medicine approaches
• Host genetic influences on microbiome
• Therapeutic target identification
• Disease susceptibility factors

Systems Biology

This research demonstrates:

• Multi-level biological integration
• Host-microbe network interactions
• Emergent system properties
• Complex trait architecture
• Holobiont perspective

Read the paper →