Author ORCID Identifier

Year of Publication


Degree Name

Doctor of Philosophy (PhD)

Document Type

Doctoral Dissertation


Arts and Sciences



First Advisor

Dr. Vincent M. Cassone


While the expression of circadian rhythms is nearly universal among multicellular eukaryotic organisms, demonstration of this phenomenon in prokaryotes has been largely restricted to photosynthetic cyanobacteria until very recently. Further, growing interest in gastrointestinal microbiomes has revealed a complex temporal relationship between the gastrointestinal clock and the bacterial microbiome within. At least one member of the gut microbiome, Klebsiella (née Enterobacter) aerogenes, responds to the indoleamine hormone melatonin, secreted by the gastrointestinal system itself. Further research revealed that K. aerogenes also expresses a circadian rhythm in motility and gene expression that is temperature compensated. Although rhythmicity is unaltered by changes in temperature, cycles of ambient temperature entrain circadian rhythms in K. aerogenes. In this work I investigated new aspects of circadian rhythmicity in Klebsiella aerogenes. I characterized new clock-controlled genes and found that circadian rhythms in this bacterium rapidly decrease in amplitude following exposure to temperature cycles irrespectively of tested luciferase reporters. I discussed and explained the mechanisms of this damping.

The next hypothesis I tested was whether this circadian rhythmicity of K. aerogenes persist in vivo within the gastrointestinal track of the host. To test this, antibiotic treated laboratory mice (a heterologous host for this bacterium) were infected with K. aerogenes. Then I determined whether the bacterium’s circadian rhythmicity was sustained by quantifying endogenous and infection bacterial DNA within the lumen of the gut. I found that K. aerogenes persisted within the gut for several days, and its abundance was rhythmic. Additionally, the quantity of total bacteria and enterobacteria was also rhythmic.

Further, for the first time I characterized transcriptome of this bacterium as the culture matures. Moreover, I investigated the transcriptional changes induced by melatonin in K. aerogenes. I demonstrated that the majority of differentially expressed genes are growth stage specific. This indole molecule affects genes related to biofilm formation, fimbria biogenesis, transcriptional regulators, carbohydrate transport and metabolism, phosphotransferase system (PTS), stress response, metal ion binding and transport. It is likely that differential expression of biofilm and fimbria related genes is responsible for differences in macrocolony area. Additionally, melatonin potentially helps Klebsiella aerogenes in host colonization.

These experiments in sum suggest a role of melatonin in modifying transcriptome of Klebsiella aerogenes and suggest its potential role in communication between the host and its commensal microbiota. Additionally, my work demonstrated rhythmicity of additional clock-controlled genes, improved experimental approach necessary to study circadian rhythmicity in K. aerogenes and helped to better understand this phenomenon.

Digital Object Identifier (DOI)

Funding Information

Department of Biology, Teaching Assistantship (Spring 2017, Fall 2020)

Research Assistantship (Fall 2016, Summer 2017, Fall 2017, Spring 2018, Summer 2018, Fall 2018, Spring 2019 Summer 2019, Fall 2019, Spring 2020, Summer 2020, Spring 2021, Summer 2021)

Department of Biology, Morgan Graduate Fellowship (1 semester-Fall 2019)

Supplemental_Video_21_luxCDABE_signal.avi (7237 kB)
Supplemental Video 2.1

Supplemental Table S31 _expo_convsstat_con.DEG.xls (653 kB)
Supplemental Table 3.1

Supplemental Table S32_expo_melvsexpo_con.DEG.xls (14 kB)
Supplemental Table 3.2

Supplemental Table S33_stat_melvsstat_con.DEG.xls (5 kB)
Supplemental Table 3.3

Supplemental Table S34_sRNA_length.xls (1 kB)
Supplemental Table 3.4