Date of Award


Document Type

Campus Access Dissertation


Chemistry and Biochemistry



First Advisor

Franklin W Outten


Biofilm formation is a complex developmental process regulated by multiple environmental signals. In addition to other nutrients, the transition metal iron can also regulate biofilm formation. Iron-dependent regulation of biofilm formation varies by bacterial species, and the exact regulatory pathways that control iron-dependent biofilm formation are often unknown or only partially characterized. To address this gap in our knowledge, we examined the role of iron availability in regulating biofilm formation in Escherichia coli. The results indicate that biofilm formation is repressed under low-iron conditions in E. coli. Furthermore, a key iron regulator, IscR, controls biofilm formation in response to changes in cellular Fe-S homeostasis. IscR regulates the FimE recombinase to control expression of type I fimbriae in E. coli. We propose that iron-dependent regulation of FimE via IscR leads to decreased surface attachment and biofilm dispersal under iron-limiting conditions.

Bacterial biofilms also tightly interact with higher organisms. The mammalian gastrointestinal tract harbors a huge number of bacterial cells, with numerous species. Those bacteria profoundly affect the host's life, including causing many diseases. To help understand its role in the colon cancer development, we compared the colonic bacterial communities from the ApcMin/+ mouse model of colon cancer to those of healthy mice, at the level of the overall community structure down to specific genera or species-level OTUs. Results from various techniques show that the bacterial distribution differences exist both on the community structures as well as specific genus/OTUs.


© 2011, Yun Wu (7881 kB)
Original raw sequences (2966 kB)
Sequences after all pre-processing (2153 kB)
other (8418 kB)
Data files after average clustering (including the alignment fasta file) (2420 kB)
All unique sequence taxonomic informaiton based on different database (258 kB)
Taxonomic informaiton for each OTU at 97% identity level