Date of Completion


Embargo Period



Termite, genomics, transcriptomics, 16s amplicon seq, protist, endosymbiont

Major Advisor

Joerg Graf

Associate Advisor

Daniel Gage

Associate Advisor

Ranjan Srivastava

Associate Advisor

J. Peter Gogarten

Associate Advisor

Jonathan Klassen

Field of Study

Molecular and Cell Biology


Doctor of Philosophy

Open Access

Open Access


The termite, Reticulitermes flavipes, is a eusocial insect with the ability to utilize a nutrient-poor diet as its sole food source. The ability of this insect to survive on this diet is strongly dependent upon its microbiota residing in the hindgut. These symbionts are single-cell eukaryotic protists, bacteria, and archaea. Although the bacterial community in the hindgut is complex existing of hundreds of OTUs, it is robust and homogenous throughout a colony as a result of trophallaxis. To better understand the avenues of importance of this tripartite symbiosis, a series of metagenomics and metatranscriptomics studies were performed.

A 16S rRNA gene sequencing analysis of termites from multiple colonies and castes was performed. The core microbiota was found to consist of 17 taxa and consistent in relative abundance across multiple colonies, but the overall microbiota was different among multiple colonies. The bacterial and protist populations were compared among multiple castes and shown to differ, suggesting differences in caste diet causes change in the hindgut community.

A temporal dietary study was performed on termites with different food sources and showed a temporal shift in the hindgut microbiota with each food source causing a different shift. Artificial neural network (ANN) analysis on the bacterial abundance data was used to create a prediction model for the microbial community and determine highly correlated taxa. The ANN suggests that it may be the low-abundant taxa driving the microbial community instead of the assumed higher-abundant organisms.

Single protist cells were isolated from the hindgut and after total nucleic acids amplification of the protists and associated bacteria, the metagenomes and metatranscriptomes were sequenced and analyzed. Metabolic expression was determined for endosymbiotic bacteria of Pyrsonympha vertens and Trichonympha agilis protists. Symbiotic-specific genes were found along with differential gene expression between the two bacteria, coinciding with different protist niches.

The data produced in this thesis adds to the knowledge of termite symbioses and provides the first description of a termite core microbiota, evidence for the driving force of low abundant bacteria through ANN, and a metatranscriptomics view into the protist-bacterial symbiosis within the overall termite symbiosis.