Host Genotype and Microbiota Contribute Asymmetrically to Transcriptional Variation in the Threespine Stickleback Gut

Abstract

Recent studies of interactions between hosts and their resident microbes have revealed important ecological and evolutionary consequences that emerge from these complex interspecies relationships, including diseases that occur when the interactions go awry. Given the preponderance of these interactions, we hypothesized that effects of the microbiota on gene expression in the developing gut—an important aspect of host biology—would be pervasive, and that these effects would be both comparable in magnitude to and contingent on effects of the host genetic background. To evaluate the effects of the microbiota, host genotype, and their interaction on gene expression in the gut of a genetically diverse, gnotobiotic host model, the threespine stickleback (Gasterosteus aculeatus), we compared RNA-seq data among 84 larval fish. Surprisingly, we found that stickleback population and family differences explained substantially more gene expression variation than the presence of microbes. Expression levels of 72 genes, however, were affected by our microbiota treatment. These genes, including many associated with innate immunity, comprise a tractable subset of host genetic factors for precise, systems-level study of host–microbe interactions in the future. Importantly, our data also suggest subtle signatures of a statistical interaction between host genotype and the microbiota on expression patterns of genetic pathways associated with innate immunity, coagulation and complement cascades, focal adhesion, cancer, and peroxisomes. These genotype-by-environment interactions may prove to be important leads to the understanding of host genetic mechanisms commonly at the root of sometimes complex molecular relationships between hosts and their resident microbes.

QTL mapping of intestinal neutrophil variation and inflammation between threespine stickleback populations reveals links to neurodegenerative disease

“…Previous work in our laboratory described phenotypic variation between freshwater and oceanic ecotype inflammatory responses, with oceanic individuals responding more robustly to the presence of microbes measured by an increase in intestinal neutrophil accumulation and changes in gene expression (Milligan-Myhre et al 2016;Small et al 2017). These findings identified a potential role of host genetic variation on differences in intestinal inflammation and the response to the presence of microbes across populations.…”

“…An F2 family (n = 64) was produced intercrossing F1 siblings. Fertilized eggs were incubated overnight in one-micron filter sterilized antibiotic embryo media containing 100 mg/mL Ampicillin, 50 mg/mL Kanamycin, and 8 mg/mL Amphotericin (Milligan-Myhre et al 2016;Small et al 2017). The next day embryos were surface sterilized using 0.003% bleach solution and 0.2% Polyvinylpyrolidone-iodine (PVP-I) solution (Western Chemical Inc.) following protocols described by Small et al 2017.…”

“…Fertilized eggs were incubated overnight in one-micron filter sterilized antibiotic embryo media containing 100 mg/mL Ampicillin, 50 mg/mL Kanamycin, and 8 mg/mL Amphotericin (Milligan-Myhre et al 2016;Small et al 2017). The next day embryos were surface sterilized using 0.003% bleach solution and 0.2% Polyvinylpyrolidone-iodine (PVP-I) solution (Western Chemical Inc.) following protocols described by Small et al 2017. Fish were raised in sterile stickleback embryo media until 9 days post fertilization (dpf) when they were moved to a 9.5 liter tank exposing them to the microbes present in the Cresko Lab fish facility.…”

“…To identify differentially expressed genes from the parental populations we used RNA-seq differentially expression analysis data from 14 dpf threespine stickleback guts obtained from Small et al 2017. To assign function to genes within each of our associated SNP boundaries, we used GeneCard v4.8.1 Build8.…”

“…We set out to map natural genetic variants associated with differences in intestinal neutrophil density using an F2-intercross genetic mapping study in threespine stickleback. We used these data to identify genomic regions that, when combined with previously published gene expression data from juvenile guts in the parental populations (Small et al 2017), identified a concordant list of candidate genes involved in host immunity. Surprisingly, we also found several genes with characterized functions in neurodegenerative diseases known to include intestinal inflammation as a secondary symptom.…”